https://wiki.geneontology.org/api.php?action=feedcontributions&user=Mi&feedformat=atomGO Wiki - User contributions [en]2024-03-29T05:04:38ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=13_March_2024_PAINT_Conference_Call&diff=8670713 March 2024 PAINT Conference Call2024-03-13T23:16:39Z<p>Mi: /* Agenda */</p>
<hr />
<div>==Present==<br />
<br />
==Agenda==<br />
<br />
===Taxon Constraint Curation ===<br />
<br />
We are correcting the taxon constraint violations in the current PAINT data using this [https://docs.google.com/spreadsheets/d/1fm2AVtvnhJoa7BUaDpg9Fc-w9cHmyzZrFZsylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are introduced during the curation. There two likely sources for the TCVs. First, these are really old annotations. Second, new TCs were added in the ontology after our last review.<br />
<br />
The violations occur in the following three main type of situations.<br />
# The IBD is annotated to an ancestral node older than the "only in" taxon, for example, "nucleus" is annotated to ''Archaea-Eukarypta''. These annotations were usually generated before the initial load of paint data to the database on 2/28/2017.<br />
# The propagation passes through an internal "never in" taxon constraint. There are quite a few terms that have "never in" relationships to Fungi or Pombe. Many of these "never in" TC need to be reviewed.<br />
# The propagation passes through a horizontal transfer event. This accounts roughly a third of the violations.<br />
<br />
How should we more efficiently handle this in the future when new TCs are added to the ontology?<br />
<br />
<br />
Discussion:<br />
*Review "never in" taxon constraints.<br />
**Some of them can be difficult.<br />
**Ask Jim to gather the information for us to review.<br />
**May need a jamboree, but we will first review it to see the scope of the work.<br />
*The HGT issue was discussed<br />
**Any really bad genome that caused the unreliability of HGT. We review Dustin's file of all HGT events (in 3/5/2024 email).<br />
**Block propagation through the HGT nodes. The question is whether all annotations should be blocked or only those in certain aspects, e.g, cellular components.<br />
<br />
==="Do not annotate" terms===<br />
<br />
In PAINT, there are annotations to terms marked as "do not annotate", e.g., "transport". We should:<br />
#prevent curators from annotating IBDs using these terms;<br />
#remove the existing IBDs with these terms.<br />
<br />
Discussion:<br />
*Add the following "do not annotate" list to the PAINT tool to not display these terms in the annotation matrix, so that they won't be used for the IBD annotation: current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.tsv<br />
*It is trickier to remove them, because they need to be replaced by a different term. <br />
**Can this be done with an automated process?<br />
**The replacement term needs to have experimental evidence. If not, the annotation is lost.<br />
**Probably gather all the annotations with these terms, organized in family ID and PTN IDs, and see how much work is involved.<br />
<br />
===GO meeting presentation===<br />
*Are we going to present?<br />
*If so, what topic?<br />
<br />
Did not discuss. Can be done offline.<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_March_2024_PAINT_Conference_Call&diff=8670613 March 2024 PAINT Conference Call2024-03-13T22:39:38Z<p>Mi: /* GO meeting presentation */</p>
<hr />
<div>==Present==<br />
<br />
==Agenda==<br />
<br />
===Taxon Constraint Curation ===<br />
<br />
We are correcting the taxon constraint violations in the current PAINT data using this [https://docs.google.com/spreadsheets/d/1fm2AVtvnhJoa7BUaDpg9Fc-w9cHmyzZrFZsylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are introduced during the curation. There two likely sources for the TCVs. First, these are really old annotations. Second, new TCs were added in the ontology after our last review.<br />
<br />
The violations occur in the following three main type of situations.<br />
# The IBD is annotated to an ancestral node older than the "only in" taxon, for example, "nucleus" is annotated to ''Archaea-Eukarypta''. These annotations were usually generated before the initial load of paint data to the database on 2/28/2017.<br />
# The propagation passes through an internal "never in" taxon constraint. There are quite a few terms that have "never in" relationships to Fungi or Pombe. Many of these "never in" TC need to be reviewed.<br />
# The propagation passes through a horizontal transfer event. This accounts roughly a third of the violations.<br />
<br />
How should we more efficiently handle this in the future when new TCs are added to the ontology?<br />
<br />
==="Do not annotate" terms===<br />
<br />
In PAINT, there are annotations to terms marked as "do not annotate", e.g., "transport". We should:<br />
#prevent curators from annotating IBDs using these terms;<br />
#remove the existing IBDs with these terms.<br />
<br />
Discussion:<br />
*Add the following "do not annotate" list to the PAINT tool to not display these terms in the annotation matrix, so that they won't be used for the IBD annotation: current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.tsv<br />
*It is trickier to remove them, because they need to be replaced by a different term. <br />
**Can this be done with an automated process?<br />
**The replacement term needs to have experimental evidence. If not, the annotation is lost.<br />
**Probably gather all the annotations with these terms, organized in family ID and PTN IDs, and see how much work is involved.<br />
<br />
===GO meeting presentation===<br />
*Are we going to present?<br />
*If so, what topic?<br />
<br />
Did not discuss. Can be done offline.<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_March_2024_PAINT_Conference_Call&diff=8670513 March 2024 PAINT Conference Call2024-03-13T22:39:19Z<p>Mi: /* "Do not annotate" terms */</p>
<hr />
<div>==Present==<br />
<br />
==Agenda==<br />
<br />
===Taxon Constraint Curation ===<br />
<br />
We are correcting the taxon constraint violations in the current PAINT data using this [https://docs.google.com/spreadsheets/d/1fm2AVtvnhJoa7BUaDpg9Fc-w9cHmyzZrFZsylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are introduced during the curation. There two likely sources for the TCVs. First, these are really old annotations. Second, new TCs were added in the ontology after our last review.<br />
<br />
The violations occur in the following three main type of situations.<br />
# The IBD is annotated to an ancestral node older than the "only in" taxon, for example, "nucleus" is annotated to ''Archaea-Eukarypta''. These annotations were usually generated before the initial load of paint data to the database on 2/28/2017.<br />
# The propagation passes through an internal "never in" taxon constraint. There are quite a few terms that have "never in" relationships to Fungi or Pombe. Many of these "never in" TC need to be reviewed.<br />
# The propagation passes through a horizontal transfer event. This accounts roughly a third of the violations.<br />
<br />
How should we more efficiently handle this in the future when new TCs are added to the ontology?<br />
<br />
==="Do not annotate" terms===<br />
<br />
In PAINT, there are annotations to terms marked as "do not annotate", e.g., "transport". We should:<br />
#prevent curators from annotating IBDs using these terms;<br />
#remove the existing IBDs with these terms.<br />
<br />
Discussion:<br />
*Add the following "do not annotate" list to the PAINT tool to not display these terms in the annotation matrix, so that they won't be used for the IBD annotation: current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.tsv<br />
*It is trickier to remove them, because they need to be replaced by a different term. <br />
**Can this be done with an automated process?<br />
**The replacement term needs to have experimental evidence. If not, the annotation is lost.<br />
**Probably gather all the annotations with these terms, organized in family ID and PTN IDs, and see how much work is involved.<br />
<br />
===GO meeting presentation===<br />
*Are we going to present?<br />
*If so, what topic?<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_March_2024_PAINT_Conference_Call&diff=8670413 March 2024 PAINT Conference Call2024-03-13T16:53:08Z<p>Mi: /* Do not annotate terms */</p>
<hr />
<div>==Present==<br />
<br />
==Agenda==<br />
<br />
===Taxon Constraint Curation ===<br />
<br />
We are correcting the taxon constraint violations in the current PAINT data using this [https://docs.google.com/spreadsheets/d/1fm2AVtvnhJoa7BUaDpg9Fc-w9cHmyzZrFZsylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are introduced during the curation. There two likely sources for the TCVs. First, these are really old annotations. Second, new TCs were added in the ontology after our last review.<br />
<br />
The violations occur in the following three main type of situations.<br />
# The IBD is annotated to an ancestral node older than the "only in" taxon, for example, "nucleus" is annotated to ''Archaea-Eukarypta''. These annotations were usually generated before the initial load of paint data to the database on 2/28/2017.<br />
# The propagation passes through an internal "never in" taxon constraint. There are quite a few terms that have "never in" relationships to Fungi or Pombe. Many of these "never in" TC need to be reviewed.<br />
# The propagation passes through a horizontal transfer event. This accounts roughly a third of the violations.<br />
<br />
How should we more efficiently handle this in the future when new TCs are added to the ontology?<br />
<br />
==="Do not annotate" terms===<br />
<br />
How to handle them.<br />
<br />
===GO meeting presentation===<br />
*Are we going to present?<br />
*If so, what topic?<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_March_2024_PAINT_Conference_Call&diff=8670213 March 2024 PAINT Conference Call2024-03-13T16:04:35Z<p>Mi: </p>
<hr />
<div>==Present==<br />
<br />
==Agenda==<br />
<br />
===Taxon Constraint Curation ===<br />
<br />
We are correcting the taxon constraint violations in the current PAINT data using this [https://docs.google.com/spreadsheets/d/1fm2AVtvnhJoa7BUaDpg9Fc-w9cHmyzZrFZsylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are introduced during the curation. There two likely sources for the TCVs. First, these are really old annotations. Second, new TCs were added in the ontology after our last review.<br />
<br />
The violations occur in the following three main type of situations.<br />
# The IBD is annotated to an ancestral node older than the "only in" taxon, for example, "nucleus" is annotated to ''Archaea-Eukarypta''. These annotations were usually generated before the initial load of paint data to the database on 2/28/2017.<br />
# The propagation passes through an internal "never in" taxon constraint. There are quite a few terms that have "never in" relationships to Fungi or Pombe. Many of these "never in" TC need to be reviewed.<br />
# The propagation passes through a horizontal transfer event. This accounts roughly a third of the violations.<br />
<br />
How should we more efficiently handle this in the future when new TCs are added to the ontology?<br />
<br />
===Do not annotate terms===<br />
<br />
How to handle them.<br />
<br />
===GO meeting presentation===<br />
*Are we going to present?<br />
*If so, what topic?<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_March_2024_PAINT_Conference_Call&diff=8670113 March 2024 PAINT Conference Call2024-03-13T15:12:18Z<p>Mi: </p>
<hr />
<div>==Present==<br />
<br />
==Agenda==<br />
<br />
===Taxon Constraint Curation ===<br />
<br />
We are correcting the taxon constraint violations in the current PAINT data using this [https://docs.google.com/spreadsheets/d/1fm2AVtvnhJoa7BUaDpg9Fc-w9cHmyzZrFZsylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are introduced during the curation. There two likely sources for the TCVs. First, these are really old annotations. Second, new TCs were added in the ontology after our last review.<br />
<br />
The violations occur in the following three main type of situations.<br />
# The IBD is annotated to an ancestral node older than the "only in" taxon, for example, "nucleus" is annotated to ''Archaea-Eukarypta''. These annotations were usually generated before the initial load of paint data to the database on 2/28/2017.<br />
# The propagation passes through an internal "never in" taxon constraint. There are quite a few terms that have "never in" relationships to Fungi or Pombe. Many of these "never in" TC need to be reviewed.<br />
# The propagation passes through a horizontal transfer event. This accounts roughly a third of the violations.<br />
<br />
How should we more efficiently handle this in the future when new TCs are added to the ontology?<br />
<br />
===GO meeting presentation===<br />
*Are we going to present?<br />
*If so, what topic?<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_March_2024_PAINT_Conference_Call&diff=8664513 March 2024 PAINT Conference Call2024-03-07T01:02:33Z<p>Mi: Created page with "==Present== ==Agenda== ===Taxon Constraint Curation === We are correcting the taxon constraint violations in the current PAINT data using this [https://docs.google.com/spreadsheets/d/1fm2AVtvnhJoa7BUaDpg9Fc-w9cHmyzZrFZsylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are introduced during the curation. There two likely sources for the TCVs. First, these are really old..."</p>
<hr />
<div>==Present==<br />
<br />
==Agenda==<br />
<br />
===Taxon Constraint Curation ===<br />
<br />
We are correcting the taxon constraint violations in the current PAINT data using this [https://docs.google.com/spreadsheets/d/1fm2AVtvnhJoa7BUaDpg9Fc-w9cHmyzZrFZsylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are introduced during the curation. There two likely sources for the TCVs. First, these are really old annotations. Second, new TCs were added in the ontology after our last review.<br />
<br />
The violations occur in the following three main type of situations.<br />
# The IBD is annotated to an ancestral node older than the "only in" taxon, for example, "nucleus" is annotated to ''Archaea-Eukarypta''. These annotations were usually generated before the initial load of paint data to the database on 2/28/2017.<br />
# The propagation passes through an internal "never in" taxon constraint. There are quite a few terms that have "never in" relationships to Fungi or Pombe. Many of these "never in" TC need to be reviewed.<br />
# The propagation passes through a horizontal transfer event. This accounts roughly a third of the violations.<br />
<br />
How should we more efficiently handle this in the future when new TCs are added to the ontology?<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_Conference_Calls&diff=86644PAINT Conference Calls2024-03-07T00:39:48Z<p>Mi: /* PAINT Conference Call Agenda and Minutes 2024 */</p>
<hr />
<div>[[Category:Reference Genome]][[Category:Archived]]<br />
The second Wednesday of each month; 9 AM Pacific time<br />
<br />
==PAINT Conference Call Agenda and Minutes 2024== <br />
* [[10 Jan 2024_PAINT_Conference_Call]]<br />
* [[14 Feb 2024_PAINT_Conference_Call]]<br />
* [[13 March 2024_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Agenda and Minutes 2023== <br />
* [[1 Feb 2023_PAINT_Conference_Call]]<br />
* [[1 March 2023_PAINT_Conference_Call]]<br />
* [[12 April 2023_PAINT_Conference_Call]]<br />
* [[17 May 2023_PAINT_Conference_Call]]<br />
* [[14 June 2023_PAINT_Conference_Call]]<br />
* [[20 September 2023_PAINT_Conference_Call]]<br />
* [[13 December 2023_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2022== <br />
* [[8 Feb 2022_PAINT_Conference_Call]]<br />
* [[20 Apr 2022_PAINT_Conference_Call]]<br />
* [[6th July 2022_PAINT_Conference_Call]]<br />
* [[3rd Aug 2022_PAINT_Conference_call]]<br />
* [[7th Sept 2022_PAINT_Conference_call]]<br />
* [[5th Oct 2022_PAINT_Conference_call]]<br />
* [[2nd Nov 2022_PAINT_Conference_call]]<br />
* [[7th Dec 2022_PAINT_Conference_call]]<br />
<br />
==PAINT Conference Call Minutes 2021== <br />
* [[5 Jan 2021_PAINT_Conference_Call]]<br />
* [[26 Jan 2021_PAINT_Conference_Call]]<br />
* [[2 Mar 2021_PAINT_Conference_Call]]<br />
* [[6 Apr 2021_PAINT_Conference_Call]]<br />
* [[27 Apr 2021_PAINT_Conference_Call]] (since May 4th is the GO meeting)<br />
* [[1 Jun 2021_PAINT_Conference_Call]]<br />
* [[6 Jul 2021_PAINT_Conference_Call]]<br />
* [[3 Aug 2021_PAINT_Conference_Call]]<br />
* [[31 Aug 2021_PAINT_Conference_Call]]<br />
* [[5 Oct 2021_PAINT_Conference_Call]]<br />
* [[2 Nov 2021_PAINT_Conference_Call]]<br />
* [[7 Dec 2021_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2020== <br />
* [[7 Jan 2020_PAINT_Conference_Call]]<br />
* [[4 Fev 2020_PAINT_Conference_Call]]<br />
* [[3 March 2020_PAINT_Conference_Call]]<br />
* [[7 April 2020_PAINT_Conference_Call]]<br />
* [[5 May 2020_PAINT_Conference_Call]]<br />
* [[2 June 2020_PAINT_Conference_Call]]<br />
* [[7 July 2020_PAINT_Conference_Call]]<br />
* [[1 September 2020_PAINT_Conference_Call]]<br />
* [[6 October 2020_PAINT_Conference_Call]]<br />
* [[10 November 2020_PAINT_Conference_Call]]<br />
* [[1 December 2020_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2019== <br />
* [[5 March 2019_PAINT_Conference_Call]]<br />
* [[2 April 2019_PAINT_Conference_Call]]<br />
* [[7 May 2019_PAINT_Conference_Call]]<br />
* [[4 June 2019_PAINT_Conference_Call]]<br />
* [[9 July 2019_PAINT_Conference_Call]]<br />
* [[13 August 2019_PAINT_Conference_Call]]<br />
* [[3 September 2019_PAINT_Conference_Call]]<br />
* [[1 October 2019_PAINT_Conference_Call]]<br />
* [[5 November 2019_PAINT_Conference_Call]]<br />
* [[3 December 2019_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2016== <br />
* [[19 January 2016_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call Minutes 2015== <br />
* [[1 December 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 November 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[21 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[16 June 2015_PAINT_Conference_call]] 8 AM Pacific<br />
* [[2 June 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[19 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[5 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 April 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 3 PM UK<br />
* [[3 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[3 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call minutes Minutes 2014==<br />
<br />
* [[16 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[2 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[23 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[9 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[26 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[12 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[8 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[24 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[10 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[13 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[1 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[25 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[11 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[25 FEB 2014_PAINT_Phone_Conference_call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[11 FEB 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[28 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[14 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2013==<br />
<br />
<br />
* [[13 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2011==<br />
* [[14 JUNE 2011_RefGen_Phone_Conference]] 8 AM Pacific, 10 AM Central, 11 AM Eastern, 4 PM UK<br />
* [[10 MAY 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[12 APR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 MAR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 FEB 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 JAN 2011_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 DEC 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
<br />
==PAINT Conference Call minutes Minutes 2010==<br />
* [[9 NOV 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* OCT 2010 CANCELED - Conflict with the Biocuration meeting<br />
* [[28 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[21 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[14 SEPT 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[10 AUG 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[13 JULY 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[8 JUN 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 MAY 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* 13 APR 2010_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[9 MAR 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[9 FEB 2010_RefGen_Phone_Conference]] 8 AM PST, 10 AM CST, 11 AM EST, 4 PM BST<br />
* [[12 JAN 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2009==<br />
* 8 Dec 2009_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[10 NOV 2009_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[13 Oct 2009_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[8 Sept 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 July 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[9 June 2009_RefGen_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
* 12May2009_RefGen_Phone_Conference CANCELED, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
*14April2009_RefGen_Phone_Conference: CANCELED, 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
*[[10March09_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 6 PM BST** Time not changed yet)<br />
*[[RefGenome10Feb09_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*RefGenome13Jan09_Phone_Conference: CANCELED<br />
<br />
==PAINT Conference Call minutes Minutes 2008==<br />
*[[RefGenome9Dec08_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*[[RefGenome11Nov08_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST)<br />
* RefGenome14Oct08_Phone_Conference: CANCELED<br />
*[[RefGenome9Sept08_Phone_Conference]]<br />
*[[RefGenome12Aug08_Phone_Conference]]<br />
*[[RefGenome8Jul08_Phone_Conference]]<br />
*[[RefGenome10Jun08_Phone_Conference]]<br />
*RefGenome13May08_Phone_Conference CANCELED<br />
*[[RefGenome8Apr08_Phone_Conference]]<br />
*[[RefGenome11Mar08_Phone_Conference]]<br />
*[[RefGenome12Feb08_Phone_Conference]]<br />
*[[RefGenome08Jan08_Phone_Conference]]<br />
<br />
==PAINT Conference Call minutes Minutes 2007==<br />
*[[RefGenome11Dec07_Phone_Conference]]<br />
*[[RefGenome13Nov07_Phone_Conference]]<br />
*[[RefGenome9Oct07_Phone_Conference]]<br />
*[[RefGenome11Sept07_Phone_Conference]]<br />
*[[RefGenome07Aug07_Phone_Conference]]<br />
*[[RefGenome10July07_Phone_Conference]]<br />
*[[RefGenome12Jun07_Phone_Conference]]<br />
<br />
<br />
<br />
[[Phylogenetic_Annotation_Project | Back to Phylogenetic Annotation Main Page]]</div>Mihttps://wiki.geneontology.org/index.php?title=14_Feb_2024_PAINT_Conference_Call&diff=8659614 Feb 2024 PAINT Conference Call2024-02-14T17:12:50Z<p>Mi: /* Present */</p>
<hr />
<div>==Present==<br />
Dustin, Marc, Anushya, Paul, Huaiyu, Pascale<br />
<br />
==Agenda==<br />
===New certificates===<br />
<br />
New certificates were installed on https://go.paint.usc.edu/ (UPL17) and https://go.paint-dev.usc.edu/ (UPL15). You will have to install the new certificate to use PAINT to view or curate families.<br />
Please refer to the certificate installation instructions on https://go.paint-dev.usc.edu/doc/Installation.jsp<br />
<br />
You should follow the instruction in section I "Save the certificate to your system." After that, use the following commands on Mac.<br />
<br />
For v.17.0 PAINT:<br />
*sudo keytool -delete -alias gopaintuscedu -keystore /Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home/lib/security/cacerts<br />
*sudo keytool -import -alias gopaintuscedu -file ~/Downloads/go-paint-usc-edu.pem -keystore /Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home/lib/security/cacerts<br />
<br />
For v.15.0 PAINT:<br />
*sudo keytool -delete -alias gopaintdevuscedu -keystore /Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home/lib/security/cacerts<br />
*sudo keytool -import -alias gopaintdevuscedu -file ~/Downloads/go-paint-dev-usc-edu.pem -keystore /Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home/lib/security/cacerts<br />
<br />
===PAINT paper===<br />
* Latest draft: https://docs.google.com/document/d/1cjIPb4LP8ifmq7k3ryECw5w9YsB8PdB_/edit<br />
* Supplemental materials: https://docs.google.com/document/d/1KN4ROPx6ddxsXOaUg5puc4LzgCtuUUYb/edit#heading=h.gjdgxs<br />
* Enrichment test site.<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=14_Feb_2024_PAINT_Conference_Call&diff=8658614 Feb 2024 PAINT Conference Call2024-02-13T20:09:39Z<p>Mi: /* New certificates */</p>
<hr />
<div>==Present==<br />
<br />
<br />
==Agenda==<br />
===New certificates===<br />
<br />
New certificates were installed on https://go.paint.usc.edu/ (UPL17) and https://go.paint-dev.usc.edu/ (UPL15). You will have to install the new certificate to use PAINT to view or curate families.<br />
Please refer to the certificate installation instructions on https://go.paint-dev.usc.edu/doc/Installation.jsp<br />
<br />
You should follow the instruction in section I "Save the certificate to your system." After that, use the following commands on Mac.<br />
<br />
For v.17.0 PAINT:<br />
*sudo keytool -delete -alias gopaintuscedu -keystore /Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home/lib/security/cacerts<br />
*sudo keytool -import -alias gopaintuscedu -file ~/Downloads/go-paint-usc-edu.pem -keystore /Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home/lib/security/cacerts<br />
<br />
For v.15.0 PAINT:<br />
*sudo keytool -delete -alias gopaintdevuscedu -keystore /Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home/lib/security/cacerts<br />
*sudo keytool -import -alias gopaintdevuscedu -file ~/Downloads/go-paint-dev-usc-edu.pem -keystore /Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home/lib/security/cacerts<br />
<br />
===PAINT paper===<br />
* Latest draft: https://docs.google.com/document/d/1cjIPb4LP8ifmq7k3ryECw5w9YsB8PdB_/edit<br />
* Supplemental materials: https://docs.google.com/document/d/1KN4ROPx6ddxsXOaUg5puc4LzgCtuUUYb/edit#heading=h.gjdgxs<br />
* Enrichment test site.<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=14_Feb_2024_PAINT_Conference_Call&diff=8658514 Feb 2024 PAINT Conference Call2024-02-13T18:34:48Z<p>Mi: /* New certificates */</p>
<hr />
<div>==Present==<br />
<br />
<br />
==Agenda==<br />
===New certificates===<br />
<br />
New certificates were installed on https://go.paint.usc.edu/ (UPL17) and https://go.paint-dev.usc.edu/ (UPL15). You will have to install the new certificate to use PAINT to view or curate families.<br />
Please refer to the certificate installation instructions on https://go.paint-dev.usc.edu/doc/Installation.jsp<br />
<br />
===PAINT paper===<br />
* Latest draft: https://docs.google.com/document/d/1cjIPb4LP8ifmq7k3ryECw5w9YsB8PdB_/edit<br />
* Supplemental materials: https://docs.google.com/document/d/1KN4ROPx6ddxsXOaUg5puc4LzgCtuUUYb/edit#heading=h.gjdgxs<br />
* Enrichment test site.<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=14_Feb_2024_PAINT_Conference_Call&diff=8658414 Feb 2024 PAINT Conference Call2024-02-13T18:29:12Z<p>Mi: Created page with "==Present== ==Agenda== ===New certificates=== Installation instructions. ===PAINT paper=== * Latest draft: https://docs.google.com/document/d/1cjIPb4LP8ifmq7k3ryECw5w9YsB8PdB_/edit * Supplemental materials: https://docs.google.com/document/d/1KN4ROPx6ddxsXOaUg5puc4LzgCtuUUYb/edit#heading=h.gjdgxs * Enrichment test site. Category:PAINT"</p>
<hr />
<div>==Present==<br />
<br />
<br />
==Agenda==<br />
===New certificates===<br />
Installation instructions.<br />
<br />
===PAINT paper===<br />
* Latest draft: https://docs.google.com/document/d/1cjIPb4LP8ifmq7k3ryECw5w9YsB8PdB_/edit<br />
* Supplemental materials: https://docs.google.com/document/d/1KN4ROPx6ddxsXOaUg5puc4LzgCtuUUYb/edit#heading=h.gjdgxs<br />
* Enrichment test site.<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=10_Jan_2024_PAINT_Conference_Call&diff=8658310 Jan 2024 PAINT Conference Call2024-02-13T18:25:43Z<p>Mi: /* Present */</p>
<hr />
<div>==Present==<br />
Marc, Dustin, Anushya, Huaiyu, Paul T., Pascale<br />
<br />
==Agenda==<br />
<br />
===GitHub Tickets===<br />
* "GOREF" vs. "GO_REF" in IBA reference column - https://github.com/geneontology/go-site/issues/2185#issuecomment-1869045297<br />
** "GOREF" is a typo. Should be "GO_REF" and needs to be fixed in both createGAF.pl script and ontobio QC IBA GORULE:0000037 test code.<br />
* Species vs. strain taxon ID for ''S. pombe'' - https://github.com/geneontology/helpdesk/issues/468<br />
<br />
===Update on automatic replacement of obsoleted GO terms in PAINT annotations===<br />
* All the missing replacement GO terms have been added back to the PAINT annotations by Anushya's validation program.<br />
* Dustin will regenerate the stats.<br />
** Total IBA annotation change: +1.53% (+58,588 annotations) - [https://docs.google.com/spreadsheets/d/13Q2zhWmwjR_GiZN8mD2yhbdC_FdukQacCMhUHFtVSxo/edit#gid=1524020448 report]<br />
** [https://docs.google.com/spreadsheets/d/1ZxWnV1f0dZT7BT8NrvY3Vv9Yd_Ft1-kuerpFiyEcCac/edit#gid=0 Missing human IBA diff - updated 20240108]<br />
<br />
===PAINT paper===<br />
<br />
We are going to focus our discussion on the new draft of human functionome paper. Here is the link to the draft.<br />
https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit?usp=sharing<br />
<br />
We will discuss new data that can possibly address reviewers' concerns. Huaiyu circulated some of them. We can discuss about them.<br />
<br />
Test website based on UPL15 for viewing Full GO IBA/IEA annotations can be accessed via https://go.paint-dev.usc.edu <br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_Conference_Calls&diff=86582PAINT Conference Calls2024-02-13T18:25:09Z<p>Mi: /* PAINT Conference Call Agenda and Minutes 2024 */</p>
<hr />
<div>[[Category:Reference Genome]][[Category:Archived]]<br />
The second Wednesday of each month; 9 AM Pacific time<br />
<br />
==PAINT Conference Call Agenda and Minutes 2024== <br />
* [[10 Jan 2024_PAINT_Conference_Call]]<br />
* [[14 Feb 2024_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Agenda and Minutes 2023== <br />
* [[1 Feb 2023_PAINT_Conference_Call]]<br />
* [[1 March 2023_PAINT_Conference_Call]]<br />
* [[12 April 2023_PAINT_Conference_Call]]<br />
* [[17 May 2023_PAINT_Conference_Call]]<br />
* [[14 June 2023_PAINT_Conference_Call]]<br />
* [[20 September 2023_PAINT_Conference_Call]]<br />
* [[13 December 2023_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2022== <br />
* [[8 Feb 2022_PAINT_Conference_Call]]<br />
* [[20 Apr 2022_PAINT_Conference_Call]]<br />
* [[6th July 2022_PAINT_Conference_Call]]<br />
* [[3rd Aug 2022_PAINT_Conference_call]]<br />
* [[7th Sept 2022_PAINT_Conference_call]]<br />
* [[5th Oct 2022_PAINT_Conference_call]]<br />
* [[2nd Nov 2022_PAINT_Conference_call]]<br />
* [[7th Dec 2022_PAINT_Conference_call]]<br />
<br />
==PAINT Conference Call Minutes 2021== <br />
* [[5 Jan 2021_PAINT_Conference_Call]]<br />
* [[26 Jan 2021_PAINT_Conference_Call]]<br />
* [[2 Mar 2021_PAINT_Conference_Call]]<br />
* [[6 Apr 2021_PAINT_Conference_Call]]<br />
* [[27 Apr 2021_PAINT_Conference_Call]] (since May 4th is the GO meeting)<br />
* [[1 Jun 2021_PAINT_Conference_Call]]<br />
* [[6 Jul 2021_PAINT_Conference_Call]]<br />
* [[3 Aug 2021_PAINT_Conference_Call]]<br />
* [[31 Aug 2021_PAINT_Conference_Call]]<br />
* [[5 Oct 2021_PAINT_Conference_Call]]<br />
* [[2 Nov 2021_PAINT_Conference_Call]]<br />
* [[7 Dec 2021_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2020== <br />
* [[7 Jan 2020_PAINT_Conference_Call]]<br />
* [[4 Fev 2020_PAINT_Conference_Call]]<br />
* [[3 March 2020_PAINT_Conference_Call]]<br />
* [[7 April 2020_PAINT_Conference_Call]]<br />
* [[5 May 2020_PAINT_Conference_Call]]<br />
* [[2 June 2020_PAINT_Conference_Call]]<br />
* [[7 July 2020_PAINT_Conference_Call]]<br />
* [[1 September 2020_PAINT_Conference_Call]]<br />
* [[6 October 2020_PAINT_Conference_Call]]<br />
* [[10 November 2020_PAINT_Conference_Call]]<br />
* [[1 December 2020_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2019== <br />
* [[5 March 2019_PAINT_Conference_Call]]<br />
* [[2 April 2019_PAINT_Conference_Call]]<br />
* [[7 May 2019_PAINT_Conference_Call]]<br />
* [[4 June 2019_PAINT_Conference_Call]]<br />
* [[9 July 2019_PAINT_Conference_Call]]<br />
* [[13 August 2019_PAINT_Conference_Call]]<br />
* [[3 September 2019_PAINT_Conference_Call]]<br />
* [[1 October 2019_PAINT_Conference_Call]]<br />
* [[5 November 2019_PAINT_Conference_Call]]<br />
* [[3 December 2019_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2016== <br />
* [[19 January 2016_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call Minutes 2015== <br />
* [[1 December 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 November 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[21 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[16 June 2015_PAINT_Conference_call]] 8 AM Pacific<br />
* [[2 June 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[19 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[5 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 April 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 3 PM UK<br />
* [[3 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[3 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call minutes Minutes 2014==<br />
<br />
* [[16 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[2 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[23 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[9 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[26 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[12 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[8 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[24 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[10 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[13 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[1 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[25 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[11 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[25 FEB 2014_PAINT_Phone_Conference_call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[11 FEB 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[28 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[14 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2013==<br />
<br />
<br />
* [[13 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2011==<br />
* [[14 JUNE 2011_RefGen_Phone_Conference]] 8 AM Pacific, 10 AM Central, 11 AM Eastern, 4 PM UK<br />
* [[10 MAY 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[12 APR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 MAR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 FEB 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 JAN 2011_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 DEC 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
<br />
==PAINT Conference Call minutes Minutes 2010==<br />
* [[9 NOV 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* OCT 2010 CANCELED - Conflict with the Biocuration meeting<br />
* [[28 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[21 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[14 SEPT 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[10 AUG 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[13 JULY 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[8 JUN 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 MAY 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* 13 APR 2010_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[9 MAR 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[9 FEB 2010_RefGen_Phone_Conference]] 8 AM PST, 10 AM CST, 11 AM EST, 4 PM BST<br />
* [[12 JAN 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2009==<br />
* 8 Dec 2009_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[10 NOV 2009_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[13 Oct 2009_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[8 Sept 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 July 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[9 June 2009_RefGen_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
* 12May2009_RefGen_Phone_Conference CANCELED, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
*14April2009_RefGen_Phone_Conference: CANCELED, 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
*[[10March09_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 6 PM BST** Time not changed yet)<br />
*[[RefGenome10Feb09_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*RefGenome13Jan09_Phone_Conference: CANCELED<br />
<br />
==PAINT Conference Call minutes Minutes 2008==<br />
*[[RefGenome9Dec08_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*[[RefGenome11Nov08_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST)<br />
* RefGenome14Oct08_Phone_Conference: CANCELED<br />
*[[RefGenome9Sept08_Phone_Conference]]<br />
*[[RefGenome12Aug08_Phone_Conference]]<br />
*[[RefGenome8Jul08_Phone_Conference]]<br />
*[[RefGenome10Jun08_Phone_Conference]]<br />
*RefGenome13May08_Phone_Conference CANCELED<br />
*[[RefGenome8Apr08_Phone_Conference]]<br />
*[[RefGenome11Mar08_Phone_Conference]]<br />
*[[RefGenome12Feb08_Phone_Conference]]<br />
*[[RefGenome08Jan08_Phone_Conference]]<br />
<br />
==PAINT Conference Call minutes Minutes 2007==<br />
*[[RefGenome11Dec07_Phone_Conference]]<br />
*[[RefGenome13Nov07_Phone_Conference]]<br />
*[[RefGenome9Oct07_Phone_Conference]]<br />
*[[RefGenome11Sept07_Phone_Conference]]<br />
*[[RefGenome07Aug07_Phone_Conference]]<br />
*[[RefGenome10July07_Phone_Conference]]<br />
*[[RefGenome12Jun07_Phone_Conference]]<br />
<br />
<br />
<br />
[[Phylogenetic_Annotation_Project | Back to Phylogenetic Annotation Main Page]]</div>Mihttps://wiki.geneontology.org/index.php?title=10_Jan_2024_PAINT_Conference_Call&diff=8637910 Jan 2024 PAINT Conference Call2024-01-08T23:07:11Z<p>Mi: /* Update on automatic replacement of obsoleted GO terms in PAINT annotations */</p>
<hr />
<div>==Present==<br />
<br />
<br />
<br />
==Agenda==<br />
<br />
===Update on automatic replacement of obsoleted GO terms in PAINT annotations===<br />
* All the missing replacement GO terms have been added back to the PAINT annotations by Anushya's validation program.<br />
* Dustin will regenerate the stats.<br />
<br />
===PAINT paper===<br />
<br />
We are going to focus our discussion on the new draft of human functionome paper. Here is the link to the draft.<br />
https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit?usp=sharing<br />
<br />
We will discuss new data that can possibly address reviewers' concerns. Huaiyu circulated some of them. We can discuss about them.<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=10_Jan_2024_PAINT_Conference_Call&diff=8637810 Jan 2024 PAINT Conference Call2024-01-08T23:02:37Z<p>Mi: </p>
<hr />
<div>==Present==<br />
<br />
<br />
<br />
==Agenda==<br />
<br />
===Update on automatic replacement of obsoleted GO terms in PAINT annotations===<br />
<br />
===PAINT paper===<br />
<br />
We are going to focus our discussion on the new draft of human functionome paper. Here is the link to the draft.<br />
https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit?usp=sharing<br />
<br />
We will discuss new data that can possibly address reviewers' concerns. Huaiyu circulated some of them. We can discuss about them.<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=10_Jan_2024_PAINT_Conference_Call&diff=8637710 Jan 2024 PAINT Conference Call2024-01-08T23:00:38Z<p>Mi: Created page with "==Present== ==Agenda== ===PAINT paper=== We are going to focus our discussion on the new draft of human functionome paper. Here is the link to the draft. https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit?usp=sharing There are some new data. Huaiyu circulated some of them. We can discuss about them. Category:PAINT"</p>
<hr />
<div>==Present==<br />
<br />
<br />
<br />
==Agenda==<br />
<br />
===PAINT paper===<br />
<br />
We are going to focus our discussion on the new draft of human functionome paper. Here is the link to the draft.<br />
https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit?usp=sharing<br />
<br />
There are some new data. Huaiyu circulated some of them. We can discuss about them.<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_Conference_Calls&diff=86376PAINT Conference Calls2024-01-08T21:37:00Z<p>Mi: </p>
<hr />
<div>[[Category:Reference Genome]][[Category:Archived]]<br />
The second Wednesday of each month; 9 AM Pacific time<br />
<br />
==PAINT Conference Call Agenda and Minutes 2024== <br />
* [[10 Jan 2024_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Agenda and Minutes 2023== <br />
* [[1 Feb 2023_PAINT_Conference_Call]]<br />
* [[1 March 2023_PAINT_Conference_Call]]<br />
* [[12 April 2023_PAINT_Conference_Call]]<br />
* [[17 May 2023_PAINT_Conference_Call]]<br />
* [[14 June 2023_PAINT_Conference_Call]]<br />
* [[20 September 2023_PAINT_Conference_Call]]<br />
* [[13 December 2023_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2022== <br />
* [[8 Feb 2022_PAINT_Conference_Call]]<br />
* [[20 Apr 2022_PAINT_Conference_Call]]<br />
* [[6th July 2022_PAINT_Conference_Call]]<br />
* [[3rd Aug 2022_PAINT_Conference_call]]<br />
* [[7th Sept 2022_PAINT_Conference_call]]<br />
* [[5th Oct 2022_PAINT_Conference_call]]<br />
* [[2nd Nov 2022_PAINT_Conference_call]]<br />
* [[7th Dec 2022_PAINT_Conference_call]]<br />
<br />
==PAINT Conference Call Minutes 2021== <br />
* [[5 Jan 2021_PAINT_Conference_Call]]<br />
* [[26 Jan 2021_PAINT_Conference_Call]]<br />
* [[2 Mar 2021_PAINT_Conference_Call]]<br />
* [[6 Apr 2021_PAINT_Conference_Call]]<br />
* [[27 Apr 2021_PAINT_Conference_Call]] (since May 4th is the GO meeting)<br />
* [[1 Jun 2021_PAINT_Conference_Call]]<br />
* [[6 Jul 2021_PAINT_Conference_Call]]<br />
* [[3 Aug 2021_PAINT_Conference_Call]]<br />
* [[31 Aug 2021_PAINT_Conference_Call]]<br />
* [[5 Oct 2021_PAINT_Conference_Call]]<br />
* [[2 Nov 2021_PAINT_Conference_Call]]<br />
* [[7 Dec 2021_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2020== <br />
* [[7 Jan 2020_PAINT_Conference_Call]]<br />
* [[4 Fev 2020_PAINT_Conference_Call]]<br />
* [[3 March 2020_PAINT_Conference_Call]]<br />
* [[7 April 2020_PAINT_Conference_Call]]<br />
* [[5 May 2020_PAINT_Conference_Call]]<br />
* [[2 June 2020_PAINT_Conference_Call]]<br />
* [[7 July 2020_PAINT_Conference_Call]]<br />
* [[1 September 2020_PAINT_Conference_Call]]<br />
* [[6 October 2020_PAINT_Conference_Call]]<br />
* [[10 November 2020_PAINT_Conference_Call]]<br />
* [[1 December 2020_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2019== <br />
* [[5 March 2019_PAINT_Conference_Call]]<br />
* [[2 April 2019_PAINT_Conference_Call]]<br />
* [[7 May 2019_PAINT_Conference_Call]]<br />
* [[4 June 2019_PAINT_Conference_Call]]<br />
* [[9 July 2019_PAINT_Conference_Call]]<br />
* [[13 August 2019_PAINT_Conference_Call]]<br />
* [[3 September 2019_PAINT_Conference_Call]]<br />
* [[1 October 2019_PAINT_Conference_Call]]<br />
* [[5 November 2019_PAINT_Conference_Call]]<br />
* [[3 December 2019_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2016== <br />
* [[19 January 2016_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call Minutes 2015== <br />
* [[1 December 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 November 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[21 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[16 June 2015_PAINT_Conference_call]] 8 AM Pacific<br />
* [[2 June 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[19 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[5 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 April 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 3 PM UK<br />
* [[3 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[3 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call minutes Minutes 2014==<br />
<br />
* [[16 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[2 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[23 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[9 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[26 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[12 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[8 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[24 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[10 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[13 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[1 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[25 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[11 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[25 FEB 2014_PAINT_Phone_Conference_call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[11 FEB 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[28 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[14 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2013==<br />
<br />
<br />
* [[13 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2011==<br />
* [[14 JUNE 2011_RefGen_Phone_Conference]] 8 AM Pacific, 10 AM Central, 11 AM Eastern, 4 PM UK<br />
* [[10 MAY 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[12 APR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 MAR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 FEB 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 JAN 2011_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 DEC 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
<br />
==PAINT Conference Call minutes Minutes 2010==<br />
* [[9 NOV 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* OCT 2010 CANCELED - Conflict with the Biocuration meeting<br />
* [[28 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[21 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[14 SEPT 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[10 AUG 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[13 JULY 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[8 JUN 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 MAY 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* 13 APR 2010_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[9 MAR 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[9 FEB 2010_RefGen_Phone_Conference]] 8 AM PST, 10 AM CST, 11 AM EST, 4 PM BST<br />
* [[12 JAN 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2009==<br />
* 8 Dec 2009_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[10 NOV 2009_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[13 Oct 2009_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[8 Sept 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 July 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[9 June 2009_RefGen_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
* 12May2009_RefGen_Phone_Conference CANCELED, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
*14April2009_RefGen_Phone_Conference: CANCELED, 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
*[[10March09_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 6 PM BST** Time not changed yet)<br />
*[[RefGenome10Feb09_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*RefGenome13Jan09_Phone_Conference: CANCELED<br />
<br />
==PAINT Conference Call minutes Minutes 2008==<br />
*[[RefGenome9Dec08_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*[[RefGenome11Nov08_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST)<br />
* RefGenome14Oct08_Phone_Conference: CANCELED<br />
*[[RefGenome9Sept08_Phone_Conference]]<br />
*[[RefGenome12Aug08_Phone_Conference]]<br />
*[[RefGenome8Jul08_Phone_Conference]]<br />
*[[RefGenome10Jun08_Phone_Conference]]<br />
*RefGenome13May08_Phone_Conference CANCELED<br />
*[[RefGenome8Apr08_Phone_Conference]]<br />
*[[RefGenome11Mar08_Phone_Conference]]<br />
*[[RefGenome12Feb08_Phone_Conference]]<br />
*[[RefGenome08Jan08_Phone_Conference]]<br />
<br />
==PAINT Conference Call minutes Minutes 2007==<br />
*[[RefGenome11Dec07_Phone_Conference]]<br />
*[[RefGenome13Nov07_Phone_Conference]]<br />
*[[RefGenome9Oct07_Phone_Conference]]<br />
*[[RefGenome11Sept07_Phone_Conference]]<br />
*[[RefGenome07Aug07_Phone_Conference]]<br />
*[[RefGenome10July07_Phone_Conference]]<br />
*[[RefGenome12Jun07_Phone_Conference]]<br />
<br />
<br />
<br />
[[Phylogenetic_Annotation_Project | Back to Phylogenetic Annotation Main Page]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_December_2023_PAINT_Conference_Call&diff=8632513 December 2023 PAINT Conference Call2023-12-14T18:59:14Z<p>Mi: /* Other topics, year end wrap up */</p>
<hr />
<div>==Present==<br />
<br />
Dustin, Anushya, Marc, Huaiyu, Pascale, Paul T.<br />
<br />
==Agenda==<br />
<br />
===Automatic replacement of obsoleted GO terms in PAINT annotations===<br />
* PAINT validator tool will start doing this during the full GO update. [https://github.com/pantherdb/features-bugs/issues/36 GH ticket]<br />
* Would this new logic affect Curation tool behavior? Editing a book invokes some validation/QC checks, which would include this obsolete term repair.<br />
** Any curation scenarios we should be thinking/worrying about?<br />
<br />
===Other topics, year end wrap up===<br />
<br />
# PAN-GO paper update<br />
# PANTHER 19, PAINT migration<br />
# Future PAINT papers<br />
## Evolution and function models - functional gain and loss at different evolution events...<br />
## Non-human MOD PAINT annotation - a comparison among yeast (single cell), fly/worm (invertebrate) and mouse...<br />
## Comparison of human and other homonid genomes<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_December_2023_PAINT_Conference_Call&diff=8632413 December 2023 PAINT Conference Call2023-12-13T17:55:23Z<p>Mi: /* Other topics, year end wrap up */</p>
<hr />
<div>==Present==<br />
<br />
Dustin, Anushya, Marc, Huaiyu, Pascale, Paul T.<br />
<br />
==Agenda==<br />
<br />
===Automatic replacement of obsoleted GO terms in PAINT annotations===<br />
* PAINT validator tool will start doing this during the full GO update. [https://github.com/pantherdb/features-bugs/issues/36 GH ticket]<br />
* Would this new logic affect Curation tool behavior? Editing a book invokes some validation/QC checks, which would include this obsolete term repair.<br />
** Any curation scenarios we should be thinking/worrying about?<br />
<br />
===Other topics, year end wrap up===<br />
<br />
# PAN-GO paper update<br />
# PANTHER 19, PAINT migration<br />
# Future PAINT papers<br />
## Evolution and function models - functional gain and loss at different evolution events...<br />
## Non-human MOD PAINT annotation - a comparison among yeast (single cell), fly/worm (invertebrate) and mouse...<br />
## Comparison of human and other homomid genomes<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_December_2023_PAINT_Conference_Call&diff=8632313 December 2023 PAINT Conference Call2023-12-13T17:44:02Z<p>Mi: /* Present */</p>
<hr />
<div>==Present==<br />
<br />
Dustin, Anushya, Marc, Huaiyu, Pascale, Paul T.<br />
<br />
==Agenda==<br />
<br />
===Automatic replacement of obsoleted GO terms in PAINT annotations===<br />
* PAINT validator tool will start doing this during the full GO update. [https://github.com/pantherdb/features-bugs/issues/36 GH ticket]<br />
* Would this new logic affect Curation tool behavior? Editing a book invokes some validation/QC checks, which would include this obsolete term repair.<br />
** Any curation scenarios we should be thinking/worrying about?<br />
<br />
===Other topics, year end wrap up===<br />
<br />
# PAN-GO paper update<br />
# PANTHER 19, PAINT migration<br />
# Future PAINT papers<br />
## Evolution and function models - functional gain and loss at different evolution events...<br />
## Non-human MOD PAINT annotation - a comparison among yeast (single cell), fly/worm (invertebrate) and mouse...<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_December_2023_PAINT_Conference_Call&diff=8632113 December 2023 PAINT Conference Call2023-12-13T16:25:41Z<p>Mi: /* Other topics, year end wrap up */</p>
<hr />
<div>==Present==<br />
<br />
<br />
==Agenda==<br />
<br />
===Automatic replacement of obsoleted GO terms in PAINT annotations===<br />
* PAINT validator tool will start doing this during the full GO update<br />
* Would this new logic affect Curation tool behavior? Editing a book invokes some validation/QC checks, which would include this obsolete term repair.<br />
** Any curation scenarios we should be thinking/worrying about?<br />
<br />
===Other topics, year end wrap up===<br />
<br />
# PAN-GO paper update<br />
# PANTHER 19, PAINT migration<br />
# Future PAINT papers<br />
## Evolution and function models - functional gain and loss at different evolution events...<br />
## Non-human MOD PAINT annotation - a comparison among yeast (single cell), fly/worm (invertebrate) and mouse...<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_December_2023_PAINT_Conference_Call&diff=8632013 December 2023 PAINT Conference Call2023-12-13T16:24:48Z<p>Mi: /* Other topics, year end wrap up */</p>
<hr />
<div>==Present==<br />
<br />
<br />
==Agenda==<br />
<br />
===Automatic replacement of obsoleted GO terms in PAINT annotations===<br />
* PAINT validator tool will start doing this during the full GO update<br />
* Would this new logic affect Curation tool behavior? Editing a book invokes some validation/QC checks, which would include this obsolete term repair.<br />
** Any curation scenarios we should be thinking/worrying about?<br />
<br />
===Other topics, year end wrap up===<br />
<br />
1. PAN-GO paper update<br />
2. PANTHER 19, PAINT migration<br />
3. Future PAINT papers<br />
* Evolution and function models - functional gain and loss at different evolution events...<br />
* Non-human MOD PAINT annotation - a comparison among yeast (single cell), fly/worm (invertebrate) and mouse...<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_December_2023_PAINT_Conference_Call&diff=8631913 December 2023 PAINT Conference Call2023-12-13T16:24:17Z<p>Mi: </p>
<hr />
<div>==Present==<br />
<br />
<br />
==Agenda==<br />
<br />
===Automatic replacement of obsoleted GO terms in PAINT annotations===<br />
* PAINT validator tool will start doing this during the full GO update<br />
* Would this new logic affect Curation tool behavior? Editing a book invokes some validation/QC checks, which would include this obsolete term repair.<br />
** Any curation scenarios we should be thinking/worrying about?<br />
<br />
===Other topics, year end wrap up===<br />
<br />
# PAN-GO paper update<br />
# PANTHER 19, PAINT migration<br />
# Future PAINT papers<br />
* Evolution and function models - functional gain and loss at different evolution events...<br />
* Non-human MOD PAINT annotation - a comparison among yeast (single cell), fly/worm (invertebrate) and mouse...<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_December_2023_PAINT_Conference_Call&diff=8628713 December 2023 PAINT Conference Call2023-12-11T22:41:46Z<p>Mi: Created page with "==Present== ==Agenda== Please suggest topics to discuss. Category:PAINT"</p>
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<div>==Present==<br />
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==Agenda==<br />
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Please suggest topics to discuss.<br />
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[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_Conference_Calls&diff=86286PAINT Conference Calls2023-12-11T22:38:27Z<p>Mi: /* PAINT Conference Call Agenda and Minutes 2023 */</p>
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<div>[[Category:Reference Genome]][[Category:Archived]]<br />
The second Wednesday of each month; 9 AM Pacific time<br />
<br />
==PAINT Conference Call Agenda and Minutes 2023== <br />
* [[1 Feb 2023_PAINT_Conference_Call]]<br />
* [[1 March 2023_PAINT_Conference_Call]]<br />
* [[12 April 2023_PAINT_Conference_Call]]<br />
* [[17 May 2023_PAINT_Conference_Call]]<br />
* [[14 June 2023_PAINT_Conference_Call]]<br />
* [[20 September 2023_PAINT_Conference_Call]]<br />
* [[13 December 2023_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2022== <br />
* [[8 Feb 2022_PAINT_Conference_Call]]<br />
* [[20 Apr 2022_PAINT_Conference_Call]]<br />
* [[6th July 2022_PAINT_Conference_Call]]<br />
* [[3rd Aug 2022_PAINT_Conference_call]]<br />
* [[7th Sept 2022_PAINT_Conference_call]]<br />
* [[5th Oct 2022_PAINT_Conference_call]]<br />
* [[2nd Nov 2022_PAINT_Conference_call]]<br />
* [[7th Dec 2022_PAINT_Conference_call]]<br />
<br />
==PAINT Conference Call Minutes 2021== <br />
* [[5 Jan 2021_PAINT_Conference_Call]]<br />
* [[26 Jan 2021_PAINT_Conference_Call]]<br />
* [[2 Mar 2021_PAINT_Conference_Call]]<br />
* [[6 Apr 2021_PAINT_Conference_Call]]<br />
* [[27 Apr 2021_PAINT_Conference_Call]] (since May 4th is the GO meeting)<br />
* [[1 Jun 2021_PAINT_Conference_Call]]<br />
* [[6 Jul 2021_PAINT_Conference_Call]]<br />
* [[3 Aug 2021_PAINT_Conference_Call]]<br />
* [[31 Aug 2021_PAINT_Conference_Call]]<br />
* [[5 Oct 2021_PAINT_Conference_Call]]<br />
* [[2 Nov 2021_PAINT_Conference_Call]]<br />
* [[7 Dec 2021_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2020== <br />
* [[7 Jan 2020_PAINT_Conference_Call]]<br />
* [[4 Fev 2020_PAINT_Conference_Call]]<br />
* [[3 March 2020_PAINT_Conference_Call]]<br />
* [[7 April 2020_PAINT_Conference_Call]]<br />
* [[5 May 2020_PAINT_Conference_Call]]<br />
* [[2 June 2020_PAINT_Conference_Call]]<br />
* [[7 July 2020_PAINT_Conference_Call]]<br />
* [[1 September 2020_PAINT_Conference_Call]]<br />
* [[6 October 2020_PAINT_Conference_Call]]<br />
* [[10 November 2020_PAINT_Conference_Call]]<br />
* [[1 December 2020_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2019== <br />
* [[5 March 2019_PAINT_Conference_Call]]<br />
* [[2 April 2019_PAINT_Conference_Call]]<br />
* [[7 May 2019_PAINT_Conference_Call]]<br />
* [[4 June 2019_PAINT_Conference_Call]]<br />
* [[9 July 2019_PAINT_Conference_Call]]<br />
* [[13 August 2019_PAINT_Conference_Call]]<br />
* [[3 September 2019_PAINT_Conference_Call]]<br />
* [[1 October 2019_PAINT_Conference_Call]]<br />
* [[5 November 2019_PAINT_Conference_Call]]<br />
* [[3 December 2019_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2016== <br />
* [[19 January 2016_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call Minutes 2015== <br />
* [[1 December 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 November 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[21 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[16 June 2015_PAINT_Conference_call]] 8 AM Pacific<br />
* [[2 June 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[19 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[5 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 April 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 3 PM UK<br />
* [[3 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[3 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call minutes Minutes 2014==<br />
<br />
* [[16 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[2 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[23 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[9 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[26 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[12 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[8 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[24 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[10 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[13 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[1 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[25 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[11 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[25 FEB 2014_PAINT_Phone_Conference_call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[11 FEB 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[28 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[14 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2013==<br />
<br />
<br />
* [[13 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2011==<br />
* [[14 JUNE 2011_RefGen_Phone_Conference]] 8 AM Pacific, 10 AM Central, 11 AM Eastern, 4 PM UK<br />
* [[10 MAY 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[12 APR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 MAR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 FEB 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 JAN 2011_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 DEC 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
<br />
==PAINT Conference Call minutes Minutes 2010==<br />
* [[9 NOV 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* OCT 2010 CANCELED - Conflict with the Biocuration meeting<br />
* [[28 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[21 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[14 SEPT 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[10 AUG 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[13 JULY 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[8 JUN 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 MAY 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* 13 APR 2010_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[9 MAR 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[9 FEB 2010_RefGen_Phone_Conference]] 8 AM PST, 10 AM CST, 11 AM EST, 4 PM BST<br />
* [[12 JAN 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2009==<br />
* 8 Dec 2009_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[10 NOV 2009_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[13 Oct 2009_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[8 Sept 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 July 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[9 June 2009_RefGen_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
* 12May2009_RefGen_Phone_Conference CANCELED, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
*14April2009_RefGen_Phone_Conference: CANCELED, 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
*[[10March09_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 6 PM BST** Time not changed yet)<br />
*[[RefGenome10Feb09_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*RefGenome13Jan09_Phone_Conference: CANCELED<br />
<br />
==PAINT Conference Call minutes Minutes 2008==<br />
*[[RefGenome9Dec08_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*[[RefGenome11Nov08_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST)<br />
* RefGenome14Oct08_Phone_Conference: CANCELED<br />
*[[RefGenome9Sept08_Phone_Conference]]<br />
*[[RefGenome12Aug08_Phone_Conference]]<br />
*[[RefGenome8Jul08_Phone_Conference]]<br />
*[[RefGenome10Jun08_Phone_Conference]]<br />
*RefGenome13May08_Phone_Conference CANCELED<br />
*[[RefGenome8Apr08_Phone_Conference]]<br />
*[[RefGenome11Mar08_Phone_Conference]]<br />
*[[RefGenome12Feb08_Phone_Conference]]<br />
*[[RefGenome08Jan08_Phone_Conference]]<br />
<br />
==PAINT Conference Call minutes Minutes 2007==<br />
*[[RefGenome11Dec07_Phone_Conference]]<br />
*[[RefGenome13Nov07_Phone_Conference]]<br />
*[[RefGenome9Oct07_Phone_Conference]]<br />
*[[RefGenome11Sept07_Phone_Conference]]<br />
*[[RefGenome07Aug07_Phone_Conference]]<br />
*[[RefGenome10July07_Phone_Conference]]<br />
*[[RefGenome12Jun07_Phone_Conference]]<br />
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[[Phylogenetic_Annotation_Project | Back to Phylogenetic Annotation Main Page]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_User_Guide&diff=86149PAINT User Guide2023-10-17T21:04:43Z<p>Mi: /* PAINT software */</p>
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<div><br />
=PAINT Overview=<br />
= PAINT (Phylogenetic Annotation and INference Tool) =<br />
PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO [[Phylogenetic Annotation Project]] to support inference of GO function terms (molecular function, cellular component and biological process) by homology.<br />
== Principles underlying PAINT ==<br />
Annotation of a gene's function by homology is often referred to as "transitive annotation", in which an experimentally-characterized function of one gene is "transferred" to another gene because of their similarity in sequence. This pairwise transfer paradigm derives from the success of sequence searching algorithms such as BLAST and Smith-Waterman. Of course, pairwise conservation of function is really due to descent from a common ancestor (homology). In other words, two sequences of sufficient length are similar because they share a common ancestor, and the reason they have a common function is most likely that they inherited that function from their common ancestor. This process can be explicitly captured using a phylogenetic model.<br />
<br />
Rather than a pairwise paradigm, PAINT uses this more accurate phylogenetic model to infer gene function by homology. PAINT annotation is intended to capture actual inferences about the evolution of gene function within a gene family: the gain, inheritance, modification and loss of function over evolutionary time. Inference is a two-step process, and involves directly annotating a phylogenetic tree. In the first step, experimental GO annotations for extant sequences are used to make inferences about when a given function may have first evolved. In PAINT, this is referred to as "up-propagation", in which ancestral genes are annotated based on information about extant sequences. In the second step, "down-propagation", ancestral annotations are used to make inferences about unannotated extant sequences, based on the principle of inheritance from the common ancestor, and allowing for modification and even loss of function during evolution.<br />
<br />
'''For a more complete description, please see the [[PAINT annotation guidelines]] and the publication on the GO Phylogenetic Annotation process, [https://www.ncbi.nlm.nih.gov/pubmed/21873635 Gaudet et al, Briefings in Bioinformatics, 2011]. '''<br />
<br />
= PAINT software =<br />
PAINT is implemented in Java by Paul Thomas's group (USC). Development of PAINT has been funded by grant GM081084 from the U.S. National Institutes of Health, and the GO Consortium grant 5U41HG002273.<br />
<br />
Software details are available in https://github.com/pantherdb/db-PAINT. Refer to https://github.com/pantherdb/db-PAINT/blob/master/README.md for implementation details.<br />
<br />
== Availability and License ==<br />
PAINT is freely available for download from the Panther website: https://go.paint.usc.edu/<br />
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PAINT software is under the license of [https://github.com/pantherdb/db-PAINT/blob/master/gopaint/GPL_LICENSE.txt GPL].<br />
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==Requirements==<br />
Java 1.8 (aka Java 8 on a Macintosh) must be installed.<br />
<br />
==Installing and configuring PAINT==<br />
PAINT is a Java application, and can be run on a either Mac or Windows. To install PAINT, download the application from: https://go.paint.usc.edu/<br />
<br />
The detailed instruction on installing and configuring the software can be found at https://go.paint.usc.edu/doc/Installation.jsp.<br />
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The entire process to install the software should take no more than 10 minutes.<br />
<br />
== Data versioning ==<br />
* Phylogenetic trees are generated for [http://pantherdb.org PANTHER version 17], released on 2022-02-23.<br />
* The GO ontology version and annotations are updated monthly. <br />
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<br />
=Using PAINT=<br />
<br />
==Launching PAINT==<br />
* On a Windows machine, run the program <code>lauchPAINT.bat</code>.<br />
* On a Mac, open a Unix terminal window, go to the directory containing the PAINT program, and execute the command: <br />
<code>sh launchPAINT.sh</code> OR <code>./launchPAINT.sh</code><br />
<br />
==Login==<br />
You are required to login before you can open a tree. The purpose is to record proper acknowledgement for all the curated annotations (of tree nodes) created by you.<br />
<br />
Go to <code>File -> Login</code>.<br />
<br />
If you just want to view the tree and annotations, you can enter <code>gouser</code> as the username. The password is filled already. This is a read-only login. You can only view the tree, but can't lock the family (see below) and curate it.<br />
<br />
If you want to curate trees, enter your username and password. If you don’t have a login and password, send an email to huaiyumi@usc.edu and request one.<br />
<br />
==Curating a gene family==<br />
The analogy is to a library. You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).<br />
<br />
===Step 1: Find and "lock" families for curation===<br />
The "lock" function is only available to a curator's account. If you login to a read-only account, e.g., with "gouser" username, you can't lock a family. You can still search a family and view it.<br />
<br />
When you lock the family, other curators won’t be able to curate them. This is to prevent people from working on the same family.<br />
[[File:PAINT_search.png|thumb|Figure 1. PAINT family search box|450px]]<br />
* Go to <code>File</code> > <code>Manage and View Books...</code><br />
**A window will pop up (Fig 1). <br />
***You can search for families by various identifiers: family ID, ancestral node (PTN) ID, Gene Symbol, Protein Identifier, Gene Identifier, or gene definition. For example, enter PTHR11409 with the "Get Book by ID" option.<br />
***Retrieve a list of all families, or just the uncurated families.<br />
***Retrieve a list of families that require review (incompletely curated).<br />
**Press the "submit" button to launch search<br />
**It normally takes a few seconds to retrieve the results.<br />
[[File:PAINT_family_search_results.png|thumb|Figure 2. PAINT family search results|450px]]<br />
* Select one or several families to lock. Fig 2 shows an example when all uncurated families are returned. There are 4 possible curation status states:<br />
**Manually curated – These are the families curated, and the curator believes that the curation is complete.<br />
**Locked – Those families are locked by a curator. The name of the curator who locks the family is shown in the Locked by column. <br />
**Partially curated – These are the families that have been curated. The curator can unlock the family and leave it as partially curated.<br />
**Require PAINT review – The previously curated paint annotations are changed due to updates in either PANTHER and GO.<br />
**Unknown – These are uncurated families.<br />
*Check the box in the <code>Lock/Unlock</code> column of the families you want to check out, and click <code>Lock or Unlock selected Books</code> button at the bottom of the panel.<br />
<br />
===Step 2: Open a family to curate===<br />
* To open a family, click <code>View Locked Books</code>, and then click the <code>View</code> button (Fig 3). If you login a read-only account, you can click the <code>View</code> button as shown in Fig 2.<br />
* A family can only be locked by a single user. If a family is already locked, you can open it in View Only mode.<br />
* You can only curate families you have locked.<br />
* Most of the families can be open in a few seconds. For families with more than 1000 genes, it can take up to 30 seconds to open.<br />
<br />
[[File:PAINT_family_opening.png|thumb|Figure 3. Opening a previously locked family.|450px]]<br />
<br />
===Step 3: Save your annotations===<br />
You can choose to save but keep the family locked so you can continue the curation later. You can also save and unlock the family. <br />
* Go to <code>File</code> > <code>Save to Database</code>. A window will pop up with the following options:<br />
**'''Cancel'''<br />
**'''Save and unlock:''' The family will be unlocked and marked as Partially Curated.<br />
**'''Save:''' The family will remain locked. The curator should do this as often as possible during the curation.<br />
**'''Save, unlock & set curated:''' The family will be marked as Manually Curated.<br />
<br />
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<br />
==Appearance and Basic Operation==<br />
===Windows===<br />
PAINT is organized into three main panels (Fig 4): <br />
[[File:PAINT-overview.png|thumb|Figure 4. Main PAINT window|500px]]<br />
* The '''upper left panel''' shows a '''[[PAINT_User_Guide#Phylogenetic_Tree |phylogenetic tree]]'''. <br />
<br />
* The '''upper right panel''' allows you to switch back and forth between (i) the '''[[PAINT_User_Guide#Annotation_matrix |Annotation Matrix]]'''; (ii) the '''[[PAINT_User_Guide#Protein_Information_table |Protein Information Table]]''' and (iii) a multiple sequence alignment '''([[PAINT_User_Guide#Multiple_sequence_alignment_.28MSA.29 |MSA]])''' of all sequences. <br />
<br />
* The '''bottom panel''' contains two tabs: '''[[PAINT_User_Guide#Annotations_window |Annotations]]''' and '''[[PAINT_User_Guide#Evidence_window |Evidence]]'''. <br />
<br />
All the tabbed panes may be resized or split out into windows.<br />
<br />
* Click on a tab (e.g., Protein Information, Evidence) to bring it to the front. <br />
* Click the icons in the tabs or the upper right corner to Undock/Dock, Minimize, Maximize, or close individual tabs or groups of tabs. <br />
* Tabs and panes may also be rearranged within a window by dragging. <br />
* Columns in the Protein Information Table can be resized.<br />
* Windows may be closed, arranged, or resized by dragging boundaries.<br />
<br />
===Recommended configuration for curation===<br />
* Bigger is better. Use as much of the monitor as you can afford. If you are using a laptop, you may wish to attach an external monitor.<br />
* Adjust the width of the window and the partition between the Tree and the Table until you are comfortable with them.<br />
<br />
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<br />
===Phylogenetic Tree===<br />
<br />
A phylogenetic tree contains nodes and branches (Fig 5). There are three types of nodes, root, internal and leaf. Leaf nodes correspond to the proteins in the tree. Root and internal nodes represent the inferred most common ancestor of the descendants. Branch length may be interpreted as time estimates between the nodes. <br />
<br />
[[File:Figure 2.png|thumb|Figure 5. PAINT phylogenetic tree|400px]]<br />
The root and internal nodes of the tree are shown as circles (speciation events) and squares (gene duplication events). If the tree has been previously curated, the nodes maybe colored in indicate the type of annotation (e.g., with inferred or experimental evidence). More details will be described in the "Making an inferrence" section of this guide. The nodes have unique identifiers that start with PTN (=PaNther Node), followed by 9 digits. Mouse over a node to see its identifier. If you right-click on a node, a menu will appear with the options to: <br />
* '''Collapse node:''' - the entire clade is collapsed to a single node (rectangle). All the descendants are hidden, but the GO term assignments to them are still available for annotation. Right-click the node again and select "Expand node" to re-expand it. <br />
* '''Reroot to node:''' - make the selected node and the root, and hide the rest of the tree. This is useful when the tree is too large. To bring back the entire tree again, use menu "Tree -> Reset Root to Main". <br />
* '''Export seq ids from leaves:''' the ids of all leave sequences descended from the node are exported to a text file<br />
* '''Prune:''' All nodes descended from the node are removed from the tree.<br />
<br />
The tree branches can be rescaled if they are too long for comfortable viewing or too short to distinguish individual nodes. The default branch scale is 50, which works for most trees. To rescale, select <code>Tree->Scale...</code> and enter a different number. <br />
<br />
====Navigating within the tree====<br />
* Click on a protein name in the tree to highlight the protein in the tree and the table. <br />
* Left-click on a node in the tree to highlight the entire clade descended from it.<br />
<br />
----<br />
<br />
===Annotation matrix===<br />
'''Note: The colors refer to the default colors in PAINT'''<br />
<br />
[[File:PAINT_main.png|thumb|Figure 6. Main PAINT window|500px]]<br />
<br />
The matrix has a row for each gene/gene product in the tree, and a column for each GO term that is directly annotated to at least one gene/gene product in the tree. The annotation matrix gives an overview of the annotations associated with any proteins in table format. It displays one of the three Gene Ontologies at a time. You can switch to a different ontology by clicking the radio button on the upper left part of the window (red arrow, Fig 6). Mouse-over the downward triangle to see the GO term (yellow circle). The terms in the annotation matrix are grouped, with the most specific terms on the left. A few very broad terms such as “protein binding” are not shown, even though they are listed in the Annotations pane.<br />
<br />
Proteins with experimental annotations (IDA, EXP, IMP, IGI, IPI, or IEP evidence codes) for a particular ontology are colored and shown in boldface (blue circles). You may select one ontology at a time to examine using the radio buttons (red arrow) at the top of the window. <br />
<br />
* Click on a protein in the tree and the corresponding row will be highlighted in the matrix. <br />
<br />
[[File:annotation_matrix_color.png|thumb|500px|Figure 7. PAINT Annotation matrix]]<br />
<br />
* The annotations of the corresponding proteins and GO terms in the matrix are shown in colored squares (Fig 7).<br />
** When you first open a tree, only the experimental annotations are shown. These are the annotations than can be used for annotating ancestral genes.<br />
*** Experimental annotations are represented by green color. If it is a direct annotation (i.e. the actual annotation is to that exact term in that column of the matrix), there is a black dot in the middle of the green square. If it is an indirect annotation (i.e. the actual annotation is to a child of the term in that column of the matrix), there is a white dot in the middle of the square.<br />
*** NOT annotations are indicated with by a red circle with a white X.<br />
** When you have annotated an ancestral node, inferred annotations are also shown in the matrix. This allows you to easily keep track of what you've already annotated.<br />
*** Inferred annotations are represented by blue color, with either a black (direct) or white (indirect) dot in the center, or X for NOT as above. <br />
<br />
* Mouse-over an annotation square to see the tool tip of the protein name and the term.<br />
* Click on the annotation square to highlight the row. All the annotations to the protein, as well as the evidences and confidence codes will be displayed in the Annotation panel (see below for more details).<br />
* Right-click (or Command-click in Mac) on the experimental annotation (green square) in the matrix will automatically highlight the inferred most recent common ancestor (MRCA) node for the term.<br />
<br />
----<br />
<br />
===Protein Information table===<br />
[[File:PAINT_protein_info.png|thumb|450px|Figure 8. Protein information table]]<br />
The phylogenetic tree is aligned with a protein information table showing additional information and linkouts to various databases ([[Media:PAINT_protein_info.png|Fig 8]]). You can adjust the relative sizes of each within the window by dragging the line in the partition separating them. Note that the identifier table contains a lot of information that can be observed by scrolling to the right.<br />
<br />
====Navigating withing the Protein Information table====<br />
<br />
* Click anywhere within a row in the table to highlight the protein in the tree and the table.<br />
* Click on one of the blue linkouts will open a link in your web browser.<br />
<br />
<br clear='all'/><br />
----<br />
<br />
===Multiple sequence alignment (MSA)===<br />
[[File:PAINT_msa.png|thumb|450px|Figure 9. Multiple Sequence Alignment view]]<br />
The trees were estimated from an MSA, which can be accessed by clicking the "MSA" button on the right panel. The default view shows the entire alignment ([[Media:PAINT_msa.png|Figure 9]]). The evolutionarily conserved part of the alignment is indicated with uppercase letters. The other less conserved region is in lowercase letters. If a sequence misses a position in the matchstate, it is called a delete state and is designated by a ''dash''. If a sequence needs to insert a position in the less conserved region in order to keep the match state region aligned, it is called an insert state and is designated by a ''dot''.<br />
<br />
The conserved columns are colored with dark blue, blue or light blue, which indicates the conservation of 80%, 60% or 40%, respectively, in the column.<br />
<br />
[[File:PAINT_MSA_domain.png|thumb|450px|Figure 10. View domains in the Multiple Sequence Alignment view]]<br />
<br />
The MSA panel can also display the following two types of data:<br />
<br />
*'''Pfam domains''' The Pfam domain data are overlaid to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Domain ([[Media:PAINT_MSA_domain.png|Figure 10]]). The domains are shown as colored bars. Mouse-over the domain bar to display a brief summary of the domain information. <br />
<br />
[[File:PAINT_MSA_key_residue.png|thumb|450px|Figure 11. View active sites in the Multiple Sequence Alignment view]]<br />
<br />
*'''Active sites''' Active site data were gathered from the UniProt and mapped to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Key Residue ([[Media:PAINT_MSA_key_residue.png|Figure 11]]). Any sequence with active site information will be displayed in bold face. Mouse over the amino acid to view active site information. Coloring is as follows:<br />
**Active site – black<br />
**Binding – Red<br />
**Metal – Orange<br />
**Multiple residue types – Magenta<br />
<br />
<br />
Toggle back and forth between the table view (“Protein Information”) and the MSA view (“MSA”) using the buttons above the table/MSA panel.<br />
<br />
Note: You can view the sequence of a hypothetical ancestral protein (node) by first collapsing the appropriate node.<br />
<br clear='all'/><br />
----<br />
<br />
===Annotations and Evidence windows===<br />
[[File:PAINT_annotation_panel.png|thumb|700px|Figure 12. The annotations window]]<br />
[[File:PAINT_evidence.jpg|thumb|400px|Figure 13. Evidence window]]<br />
To view the annotations associated with a specific protein, click on that protein in the tree or table. Annotations appear in the <code>Annotation pane</code> ([[Media:PAINT_annotation_panel.png|Fig 12]]), containing the following information:<br />
* '''ECO (Evidence code):''' The type evidence code supporting the annotation. <br />
* '''Term name:''' The GO term name and accession. Clicking on the term links out to [http://amigo.geneontology.org/amigo AmiGO]. A term with a NOT annotation is displayed as strikethrough text. <br />
* '''Reference:''' The reference supporting the annotation. Clicking on the reference links out to PubMed. IBA annotations display an internal reference, PAINT_REF:00nnnnn, where nnnnn is the numerical part of the Panther family ID. <br />
* '''With:''' This column contains the evidence to support the inference. <br />
* '''Qualifiers:''' The qualifiers 'NOT', 'colocalizes_with' and 'contributes_to' each have a column in the annotation table, and a checkbox that is checked when the qualifier is present.<br />
* '''Delete:''' This is used to remove an inference made by PAINT (see [[PAINT_User_Guide#Removing_an_IBD_annotation|Removing an IBD annotation section]] below).<br />
<br />
===Evidence window===<br />
<br />
The evidence window ([[Media:PAINT_evidence.jpg|Fig 13]]) displayed automatically generated logs of the tree curation, such as annotations, validation and changes made by the PAINT pipeline upon data release.<br />
<br />
----<br />
<br />
===Curator notes===<br />
<br />
The <code>Curator notes</code> is a text editor used to record notes on the curation process. <code>Curator notes</code> can be modified by going to the <code>File</code> > <code>Update comment</code> menu.<br />
'''NOTE: The purpose of the annotation notes is to convey important points about the annotations and the phylogenetic tree both to other annotators and to users''', so annotators should try to make the notes as clear as possible. <br />
<br />
The annotator may use the Curator notes to describe important points in the annotation process, including: <br />
* References used to annotate the family (for example, a few major reviews)<br />
* Any important points about the family topology, including potential inconsistencies in the tree<br />
* Reasons for annotating to a different node than the MRCA (most common recent ancestor), ie the node that triangulation of annotation identifies. <br />
* Link to GitHub tickets leading to review of the tree annotation.<br />
<br />
----<br />
==PAINT navigation functionality==<br />
<br />
===“Find” function===<br />
[[File:PAINT_Find.jpg|thumb|400px|Figure 14. PAINT 'Find' functionality]]<br />
The Find function (<code>Edit</code> > <code>Find…</code>, Fig 14A) allows you to search for either a gene or a GO term. Select a gene or term search using the radio buttons (Fig 14B). Searches are case-insensitive.<br />
<br />
A gene search matches against exact match of any text stored in the database, such as any sequence identifiers, gene symbol, or even gene name (red arrow, Fig 14C). The search does not return partial match (blue arrow, (Fig 14C). To do a partial match, wildcard character(s) (*) can be added before and/or after the search term. Scroll through the list of matches and click on a specific match to highlight it in the tree, table, and annotation matrix, and to display its annotations in the Annotations window.<br />
<br />
You may search GO terms using text, or you may use numbers to search for GO IDs.<br />
<br clear='all'/><br />
----<br />
<br />
==Making an inference: Transferring annotations==<br />
Ancestral nodes in the tree can be annotated with any GO term that has been experimentally annotated to one (or more) of its descendants. These “inferred” annotations can be propagated to its other descendants.<br />
===Annotating an ancestral node, and propagating to descendants by inheritance===<br />
[[File:Fig13 triangulation.jpg|thumb|450px|Figure 15A. PTHR43114 before annotation]]<br />
<br />
* In the example shown in Fig 15A, 5 proteins are annotated by EXP to the GO term <code>adenine deaminase activity</code> (green squares in the 1st column of the Annotation Matrix, indicated by the red downward arrow). <br />
<br />
'''Tip:''' To view the last common ancestor that can be annotated based on triangulation(*), right click on a GO term, or anywhere in the column that contains that GO term. An inferred node, as well as its descendants, will be highlighted in grey (blue arrow, Fig 15A). <br />
* (*) '''Triangulation''' is the calculation of the last common ancestor of two sequences; in this case PAINT calculates the last common ancestor supporting an annotation to the same GO term. <br />
* Note that the node calculated by triangulation may not be the best on to annotate: the curator can decide to annotate to an more ancient or a more recent ancestor, dependent on other evidence. For example, annotations in other GO aspects may support an earlier annotation than suggested by the triangulation.<br />
* The curator should not assume that the genes in the tree are fully curated with repsect to the primary literature. It may be useful to review other papers, including reviews, to ensure annotations found in the tree accurately represents the current state of knowledge. <br />
<br />
====To annotate an ancestral node====<br />
[[File:Fig15B.jpg|thumb|450px|Figure 15B. PTHR43114 after annotation]]<br />
# Click a GO term (green square) from the Annotation Matrix (Fig. 15B) (or anywhere in the column containing the GO term).<br />
# Drag the term to the ancestral node you wish to annotate. This can be the inferred node or any other nodes. When you mouse over it, a <code>+ sign</code> will be visible next to the node. Release the mouse button to annotate. Click here for a video demo of the procedure: http://youtu.be/8kHrdiuNfos.<br />
# The node is now annotated with that term using the evidence code “IBD” (“Inferred from Biological Descendant”) (Fig. 15B).<br />
# PAINT then automatically propagates the IBD annotation to all descendants of the PAINTEed node, such that all descendants of the node will now be annotated with that term using the evidence code “IBA” (“Inferred from Biological Ancestor”). (Proteins and nodes already annotated with the term or one of its descendant terms will remain unchanged.)<br />
<br />
====Annotating an ancestral node with a qualifier====<br />
[[File:Propagating qualifiers.jpg|thumb|800px|Figure 16. Propagating qualifiers]]<br />
* If you propagate an experimental annotation that has a qualifier, ie. "NOT", "contributes_to" (for MF annotations), or "colocalizes_with" (for CC annotations), the qualifier will also get propagated, unless there are contradictory annotations, ie, annotations ''with'' and annotations ''without'' the qualifier (for the same or for different genes). In that case, a pop-up window will appear to specify whether the annotations with or without the qualifier(s) should be propagated. Click the appropriate radio button, and click on the <code>Continue</code> box to apply the selection (Fig 16).<br />
<br />
=====Notes=====<br />
* You may only annotate a node with a given GO term if '''at least one descendant''' has an annotation to that term or a child term. If you try to propagate a term with no supporting annotation, the node will turn red, and the propagation cannot be made.<br />
* Effectively, the PAINT curator only makes IBD annotations; IBA annotations are generated automatically to all descendants of the node to which an IBD annotation is made.<br />
* The IBD annotation automatically includes evidence for each of the sequences having an EXP annotation to the term or one if its descendants; it is not necessary to propagate individual EXP to generate the evidence for the annotation.<br />
<br />
===Negation of annotations: "NOT" statements===<br />
Background: Since PAINT is a model of the family's evolution, adding a NOT modifier to a descendant (either another node or a leaf) represents a loss of function during evolution, that is, we are stating that the specified function was present in an ancestral protein and has been ''lost'' in the indicated protein or clade. This is a special case of the GO guidelines for NOT, which state that a NOT annotation may be made in situations where a particular function may be expected but is absent.<br />
<br />
PAINT defines two reasons for an evolutionary loss of function, described with two separate evidence codes (ECO): <br />
* IRD = '''I'''nferred from '''R'''apid '''D'''ivergence from ancestral sequence evidence used in manual assertion: Used when there is a long branch, often following a duplication, and significant sequence divergence. For very divergent sequences, predictions are less reliable, even in the presence of a common ancestor. <br />
* IKR = '''I'''nferred from phylogenetic determination of loss of '''K'''ey '''R'''esidues evidence: Used when a residue known to be required for the activity of the protein has mutated. <br />
<br />
In both cases, the node (intermediate or leaf) on which the NOT annotation is placed gets the evidence code selected (IKR or IRD), and descendants, if any, are annotated with the IBA evidence. <br />
<br />
====To add the NOT qualifier to IBD annotations====<br />
[[File:Fig15A.jpg|thumb|450px|Figure 17A. Tree annotated with an IBD]]<br />
[[File:Fig15B.jpg|thumb|450px|Figure 17B. Pop up window to select NOT evidence]]<br />
# From a tree annotated with a IBD annotation (Fig 17A), select a node or protein to be negated. This may be either a directly annotated node or one of its children.<br />
# Click the checkbox in the NOT column of the Annotations window. <br />
# A popup menu will appear (Fig 17B). In the menu <code>Select evidence code for NOT annotation</code>, select one of the radio buttons: <br />
#* NOT due to rapid divergence<br />
#* NOT due to change in key residue(s)<br />
# '''Optional:''' In the box labeled <code>Please enter PMID and select sequence(s) from descendants providing evidence</code>, you may enter data not captured by primary annotation that support the negation. For example if a paper shows that one of the descendants does not have an activity, you can enter the PMID and select which gene was <br />
# '''Optional:''' If appropriate, you may select from the list under <code>Annotate to an ancestor term?</code>, a more general GO term to propagate to the node or sequence instead of the term negated.<br />
* In addition to the annotation no longer propagating downward, a small hash mark will appear near the node in the tree to indicate that the block exists (visible in Fig 15C). Note that a hash mark only indicates the existence of at least one NOT annotation, not that every annotation through that node is negated.<br />
<br />
'''Annotations propagated:'''<br />
[[File:Fig15C.jpg|thumb|450px|Figure 17C. Intermediate node annotated with NOT by IRK. Descendants are annotated with a NOT qualifier and IBA evidence]]<br />
[[File:Fig15D.jpg|thumb|450px|Figure 17D. Leaf node annotated with NOT by IRK.]]<br />
* If the NOT is on a node with descendants, the node will get the evidence code select (IKR or IBD), and the descendants will get an IBA evidence (Fig 17C). <br />
* If the NOT is on a leaf node it will get the evidence code select (IKR or IBD) (Fig 17D).<br />
* Upon export of PAINT annotations:<br />
** Annotations with IKR and all NOT annotations to proteins descended from that node will have the NOT qualifier added (as these have good evidence for loss of function).<br />
** Annotations with IRD and all NOT annotations to proteins descended from that node, no annotation will be exported. Thus this acts like a STOP PROPAGATION.<br />
<br />
==Removing IBD, IKR and IRD annotations==<br />
# Click on the desired node. Nodes with inferred annotations are colored orange.<br />
# Go to the Annotation tab and click the <code>Delete</code> in the Delete column (shown in a red square in Fig 13B).<br />
<br />
'''Notes:'''<br />
* Annotations and qualifiers can only be removed from the specific node to which they were made.<br />
* Primary annotations may be be changed; they may be disputed in the [https://github.com/geneontology/go-annotation/issues GO GitHub go-annotation repo].<br />
<br />
== Partial annotation of trees ==<br />
<br />
<br />
[[File:PTHR24073-RabFamily.jpg|thumb|500px|Figure 18. The RAB GTPase superfamily]]]<br />
<br />
<br />
When you want to annotate a very large family, e.g. the RAB GTPase superfamily (PTHR24073) (Fig 18), it may not be feasible to annotate all clades at the same time. In this kind of situation, you may choose to annotate only the clades you are knowledgeable and confident of, and leave other clades unexamined. When you do this, you should fully annotate the clades you choose to annotate. For example, if you choose to do the IFT27 clade, do it fully. Please don't do piecemeal annotations in various locations that may make it hard for a subsequent annotator to understand what has been done. <br />
<br />
We also agreed at the July 2014 PAINT Jamboree that you can make propagations all the way to the root if you feel that there is an ancestral role, even if you think that some clades have lost this. For example, in the RAB GTPase superfamily, we think that it had an ancestral function as a GTPase, but it is possible that some clades, e.g. the IFT22 clade, have lost this ancestral activity. You can make these high level propagations as part of your initial annotation of the family. If there are clades where this is wrong, perhaps the IBA annotation from PAINT will generate feedback that will help us correct it.<br />
<br />
=== Recording partial annotation in the notes file ===<br />
If you only partially annotate a tree, please record in the notes file which clades you have worked on using the node number, e.g. '''Eukaryota_PTN001180007''' as well as a common name, e.g. '''IFT27''', if it is helpful.<br />
<br />
==Recording trees examined, but not annotated==<br />
<br />
When you examine a tree and feel that it should not be annotated for some reason, please record that in the Evidence Notes so that we can track the fact that the family has been examined. Please use one of these tags (in all caps) in the Notes section of the Evidence tab. You can additional information after the tag if you wish (syntax between tag and additional info not discussed or determined). Then, save your annotations as normal so that PAINT will save the notes file.<br />
<br />
* '''MISSING ANNOTATION''' - Use this if the tree looks OK, but there are insufficient experimental annotations to propagate any annotations.<br />
* '''MISSING SEQUENCE''' - Use this if you feel that a specific sequence or sequences is missing. You can list the IDs of the sequence(s) after the tag.<br />
* '''BAD TREE''' - Use this if you feel that the tree has major problems beyond one or a few missing sequences.<br />
<br />
----<br />
=Interpreting the PANTHER trees=<br />
==Speciation and duplication events, and horizontal transfer==<br />
In the tree, a speciation node is shown with a circle, and a gene duplication node with an square. Horizontal transfer events also appear in the tree, though more rarely, and these are represented with a diamond.<br />
<br />
==Branch lengths==<br />
* Branch lengths show the amount of sequence divergence that has occurred between a given node and its ancestral node, in terms of the average number of amino acid substitutions per site. Shorter branches indicate less sequence divergence and therefore greater conservation of ancestral characters. A branch might be shorter because of a slower evolutionary rate (greater negative selection), or because less "time" has gone by (actually a combination of number of generations and population dynamics), or both.<br />
* Very long branches indicate an unreliable divergence estimate, due to insufficient data. Note that sometimes there is not enough data to compare all branches that descend from a given node. In this case, we have set all descendant branches to a length of 2.0 (very long branches). Branch lengths of 2.0 are often due to a sequence fragment, and at a duplication node it may also indicate a gene that has been incorrectly broken into two different genes by a gene prediction program.<br />
* Following a gene duplication (after a square node), the relative branch lengths for descendant branches are particularly useful: the shortest branch (least diverged) is more likely to have greater functional conservation.<br />
<br />
==Multiple sequence alignment (MSA)==<br />
* Some columns in the MSA have upper-case characters (and dashes '-' for insertions/deletions). These columns were used to estimate the phylogenetic tree.<br />
* Lower-case characters and periods (‘.’ for insertions/deletions) denote positions that were ignored when estimating the phylogenetic tree. Sometimes, tree errors arise because not enough columns were used, and the phylogeny could not be reconstructed well based on the included columns. Since they were not used in the phylogeny, lower-case characters can be particularly helpful in verifying the tree topology: any conserved insertions should be parsimoniously traceable to a common ancestor.<br />
<br />
----<br />
=Reporting bugs or likely errors in the trees=<br />
<br />
==Tree issues==<br />
Most often, the errors in phylogenetic trees are due to problems with the sequence alignment, or the specific MSA columns used to estimate the phylogeny. The phylogeny inference program performs fairly robust handling of sequence fragments, but sequence fragments still cause errors. Another source of error is when the sequences evolve very slowly, generating little variation from which to estimate phylogeny. In this case, the errors can usually be fixed by including additional alignment positions to consider in the phylogeny. <br />
<br />
'''If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues'''<br />
<br />
==PAINT issues==<br />
'''Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues'''<br />
<br />
=Curation Guidelines=<br />
<br />
'''Those guidelines have been published (Gaudet, Livestone, Lewis, Thomas, 2011) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059/?tool=pubmed]'''<br />
<br />
<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2021-07-01<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_User_Guide&diff=86148PAINT User Guide2023-10-17T20:58:22Z<p>Mi: /* Step 2: Open a family to curate */</p>
<hr />
<div><br />
=PAINT Overview=<br />
= PAINT (Phylogenetic Annotation and INference Tool) =<br />
PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO [[Phylogenetic Annotation Project]] to support inference of GO function terms (molecular function, cellular component and biological process) by homology.<br />
== Principles underlying PAINT ==<br />
Annotation of a gene's function by homology is often referred to as "transitive annotation", in which an experimentally-characterized function of one gene is "transferred" to another gene because of their similarity in sequence. This pairwise transfer paradigm derives from the success of sequence searching algorithms such as BLAST and Smith-Waterman. Of course, pairwise conservation of function is really due to descent from a common ancestor (homology). In other words, two sequences of sufficient length are similar because they share a common ancestor, and the reason they have a common function is most likely that they inherited that function from their common ancestor. This process can be explicitly captured using a phylogenetic model.<br />
<br />
Rather than a pairwise paradigm, PAINT uses this more accurate phylogenetic model to infer gene function by homology. PAINT annotation is intended to capture actual inferences about the evolution of gene function within a gene family: the gain, inheritance, modification and loss of function over evolutionary time. Inference is a two-step process, and involves directly annotating a phylogenetic tree. In the first step, experimental GO annotations for extant sequences are used to make inferences about when a given function may have first evolved. In PAINT, this is referred to as "up-propagation", in which ancestral genes are annotated based on information about extant sequences. In the second step, "down-propagation", ancestral annotations are used to make inferences about unannotated extant sequences, based on the principle of inheritance from the common ancestor, and allowing for modification and even loss of function during evolution.<br />
<br />
'''For a more complete description, please see the [[PAINT annotation guidelines]] and the publication on the GO Phylogenetic Annotation process, [https://www.ncbi.nlm.nih.gov/pubmed/21873635 Gaudet et al, Briefings in Bioinformatics, 2011]. '''<br />
<br />
= PAINT software =<br />
PAINT is implemented in Java by Paul Thomas's group (USC). Development of PAINT has been funded by grant GM081084 from the U.S. National Institutes of Health, and the GO Consortium grant 5U41HG002273.<br />
<br />
Software details are available in https://github.com/pantherdb/db-PAINT. Refer to https://github.com/pantherdb/db-PAINT/blob/master/README.md for implementation details.<br />
<br />
== Availability ==<br />
PAINT is freely available for download from the Panther website: https://go.paint.usc.edu/<br />
<br />
==Requirements==<br />
Java 1.8 (aka Java 8 on a Macintosh) must be installed.<br />
<br />
==Installing and configuring PAINT==<br />
PAINT is a Java application, and can be run on a either Mac or Windows. To install PAINT, download the application from: https://go.paint.usc.edu/<br />
<br />
The detailed instruction on installing and configuring the software can be found at https://go.paint.usc.edu/doc/Installation.jsp.<br />
<br />
The entire process to install the software should take no more than 10 minutes.<br />
<br />
== Data versioning ==<br />
* Phylogenetic trees are generated for [http://pantherdb.org PANTHER version 17], released on 2022-02-23.<br />
* The GO ontology version and annotations are updated monthly. <br />
<br />
----<br />
<br />
=Using PAINT=<br />
<br />
==Launching PAINT==<br />
* On a Windows machine, run the program <code>lauchPAINT.bat</code>.<br />
* On a Mac, open a Unix terminal window, go to the directory containing the PAINT program, and execute the command: <br />
<code>sh launchPAINT.sh</code> OR <code>./launchPAINT.sh</code><br />
<br />
==Login==<br />
You are required to login before you can open a tree. The purpose is to record proper acknowledgement for all the curated annotations (of tree nodes) created by you.<br />
<br />
Go to <code>File -> Login</code>.<br />
<br />
If you just want to view the tree and annotations, you can enter <code>gouser</code> as the username. The password is filled already. This is a read-only login. You can only view the tree, but can't lock the family (see below) and curate it.<br />
<br />
If you want to curate trees, enter your username and password. If you don’t have a login and password, send an email to huaiyumi@usc.edu and request one.<br />
<br />
==Curating a gene family==<br />
The analogy is to a library. You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).<br />
<br />
===Step 1: Find and "lock" families for curation===<br />
The "lock" function is only available to a curator's account. If you login to a read-only account, e.g., with "gouser" username, you can't lock a family. You can still search a family and view it.<br />
<br />
When you lock the family, other curators won’t be able to curate them. This is to prevent people from working on the same family.<br />
[[File:PAINT_search.png|thumb|Figure 1. PAINT family search box|450px]]<br />
* Go to <code>File</code> > <code>Manage and View Books...</code><br />
**A window will pop up (Fig 1). <br />
***You can search for families by various identifiers: family ID, ancestral node (PTN) ID, Gene Symbol, Protein Identifier, Gene Identifier, or gene definition. For example, enter PTHR11409 with the "Get Book by ID" option.<br />
***Retrieve a list of all families, or just the uncurated families.<br />
***Retrieve a list of families that require review (incompletely curated).<br />
**Press the "submit" button to launch search<br />
**It normally takes a few seconds to retrieve the results.<br />
[[File:PAINT_family_search_results.png|thumb|Figure 2. PAINT family search results|450px]]<br />
* Select one or several families to lock. Fig 2 shows an example when all uncurated families are returned. There are 4 possible curation status states:<br />
**Manually curated – These are the families curated, and the curator believes that the curation is complete.<br />
**Locked – Those families are locked by a curator. The name of the curator who locks the family is shown in the Locked by column. <br />
**Partially curated – These are the families that have been curated. The curator can unlock the family and leave it as partially curated.<br />
**Require PAINT review – The previously curated paint annotations are changed due to updates in either PANTHER and GO.<br />
**Unknown – These are uncurated families.<br />
*Check the box in the <code>Lock/Unlock</code> column of the families you want to check out, and click <code>Lock or Unlock selected Books</code> button at the bottom of the panel.<br />
<br />
===Step 2: Open a family to curate===<br />
* To open a family, click <code>View Locked Books</code>, and then click the <code>View</code> button (Fig 3). If you login a read-only account, you can click the <code>View</code> button as shown in Fig 2.<br />
* A family can only be locked by a single user. If a family is already locked, you can open it in View Only mode.<br />
* You can only curate families you have locked.<br />
* Most of the families can be open in a few seconds. For families with more than 1000 genes, it can take up to 30 seconds to open.<br />
<br />
[[File:PAINT_family_opening.png|thumb|Figure 3. Opening a previously locked family.|450px]]<br />
<br />
===Step 3: Save your annotations===<br />
You can choose to save but keep the family locked so you can continue the curation later. You can also save and unlock the family. <br />
* Go to <code>File</code> > <code>Save to Database</code>. A window will pop up with the following options:<br />
**'''Cancel'''<br />
**'''Save and unlock:''' The family will be unlocked and marked as Partially Curated.<br />
**'''Save:''' The family will remain locked. The curator should do this as often as possible during the curation.<br />
**'''Save, unlock & set curated:''' The family will be marked as Manually Curated.<br />
<br />
----<br />
<br />
==Appearance and Basic Operation==<br />
===Windows===<br />
PAINT is organized into three main panels (Fig 4): <br />
[[File:PAINT-overview.png|thumb|Figure 4. Main PAINT window|500px]]<br />
* The '''upper left panel''' shows a '''[[PAINT_User_Guide#Phylogenetic_Tree |phylogenetic tree]]'''. <br />
<br />
* The '''upper right panel''' allows you to switch back and forth between (i) the '''[[PAINT_User_Guide#Annotation_matrix |Annotation Matrix]]'''; (ii) the '''[[PAINT_User_Guide#Protein_Information_table |Protein Information Table]]''' and (iii) a multiple sequence alignment '''([[PAINT_User_Guide#Multiple_sequence_alignment_.28MSA.29 |MSA]])''' of all sequences. <br />
<br />
* The '''bottom panel''' contains two tabs: '''[[PAINT_User_Guide#Annotations_window |Annotations]]''' and '''[[PAINT_User_Guide#Evidence_window |Evidence]]'''. <br />
<br />
All the tabbed panes may be resized or split out into windows.<br />
<br />
* Click on a tab (e.g., Protein Information, Evidence) to bring it to the front. <br />
* Click the icons in the tabs or the upper right corner to Undock/Dock, Minimize, Maximize, or close individual tabs or groups of tabs. <br />
* Tabs and panes may also be rearranged within a window by dragging. <br />
* Columns in the Protein Information Table can be resized.<br />
* Windows may be closed, arranged, or resized by dragging boundaries.<br />
<br />
===Recommended configuration for curation===<br />
* Bigger is better. Use as much of the monitor as you can afford. If you are using a laptop, you may wish to attach an external monitor.<br />
* Adjust the width of the window and the partition between the Tree and the Table until you are comfortable with them.<br />
<br />
----<br />
<br />
===Phylogenetic Tree===<br />
<br />
A phylogenetic tree contains nodes and branches (Fig 5). There are three types of nodes, root, internal and leaf. Leaf nodes correspond to the proteins in the tree. Root and internal nodes represent the inferred most common ancestor of the descendants. Branch length may be interpreted as time estimates between the nodes. <br />
<br />
[[File:Figure 2.png|thumb|Figure 5. PAINT phylogenetic tree|400px]]<br />
The root and internal nodes of the tree are shown as circles (speciation events) and squares (gene duplication events). If the tree has been previously curated, the nodes maybe colored in indicate the type of annotation (e.g., with inferred or experimental evidence). More details will be described in the "Making an inferrence" section of this guide. The nodes have unique identifiers that start with PTN (=PaNther Node), followed by 9 digits. Mouse over a node to see its identifier. If you right-click on a node, a menu will appear with the options to: <br />
* '''Collapse node:''' - the entire clade is collapsed to a single node (rectangle). All the descendants are hidden, but the GO term assignments to them are still available for annotation. Right-click the node again and select "Expand node" to re-expand it. <br />
* '''Reroot to node:''' - make the selected node and the root, and hide the rest of the tree. This is useful when the tree is too large. To bring back the entire tree again, use menu "Tree -> Reset Root to Main". <br />
* '''Export seq ids from leaves:''' the ids of all leave sequences descended from the node are exported to a text file<br />
* '''Prune:''' All nodes descended from the node are removed from the tree.<br />
<br />
The tree branches can be rescaled if they are too long for comfortable viewing or too short to distinguish individual nodes. The default branch scale is 50, which works for most trees. To rescale, select <code>Tree->Scale...</code> and enter a different number. <br />
<br />
====Navigating within the tree====<br />
* Click on a protein name in the tree to highlight the protein in the tree and the table. <br />
* Left-click on a node in the tree to highlight the entire clade descended from it.<br />
<br />
----<br />
<br />
===Annotation matrix===<br />
'''Note: The colors refer to the default colors in PAINT'''<br />
<br />
[[File:PAINT_main.png|thumb|Figure 6. Main PAINT window|500px]]<br />
<br />
The matrix has a row for each gene/gene product in the tree, and a column for each GO term that is directly annotated to at least one gene/gene product in the tree. The annotation matrix gives an overview of the annotations associated with any proteins in table format. It displays one of the three Gene Ontologies at a time. You can switch to a different ontology by clicking the radio button on the upper left part of the window (red arrow, Fig 6). Mouse-over the downward triangle to see the GO term (yellow circle). The terms in the annotation matrix are grouped, with the most specific terms on the left. A few very broad terms such as “protein binding” are not shown, even though they are listed in the Annotations pane.<br />
<br />
Proteins with experimental annotations (IDA, EXP, IMP, IGI, IPI, or IEP evidence codes) for a particular ontology are colored and shown in boldface (blue circles). You may select one ontology at a time to examine using the radio buttons (red arrow) at the top of the window. <br />
<br />
* Click on a protein in the tree and the corresponding row will be highlighted in the matrix. <br />
<br />
[[File:annotation_matrix_color.png|thumb|500px|Figure 7. PAINT Annotation matrix]]<br />
<br />
* The annotations of the corresponding proteins and GO terms in the matrix are shown in colored squares (Fig 7).<br />
** When you first open a tree, only the experimental annotations are shown. These are the annotations than can be used for annotating ancestral genes.<br />
*** Experimental annotations are represented by green color. If it is a direct annotation (i.e. the actual annotation is to that exact term in that column of the matrix), there is a black dot in the middle of the green square. If it is an indirect annotation (i.e. the actual annotation is to a child of the term in that column of the matrix), there is a white dot in the middle of the square.<br />
*** NOT annotations are indicated with by a red circle with a white X.<br />
** When you have annotated an ancestral node, inferred annotations are also shown in the matrix. This allows you to easily keep track of what you've already annotated.<br />
*** Inferred annotations are represented by blue color, with either a black (direct) or white (indirect) dot in the center, or X for NOT as above. <br />
<br />
* Mouse-over an annotation square to see the tool tip of the protein name and the term.<br />
* Click on the annotation square to highlight the row. All the annotations to the protein, as well as the evidences and confidence codes will be displayed in the Annotation panel (see below for more details).<br />
* Right-click (or Command-click in Mac) on the experimental annotation (green square) in the matrix will automatically highlight the inferred most recent common ancestor (MRCA) node for the term.<br />
<br />
----<br />
<br />
===Protein Information table===<br />
[[File:PAINT_protein_info.png|thumb|450px|Figure 8. Protein information table]]<br />
The phylogenetic tree is aligned with a protein information table showing additional information and linkouts to various databases ([[Media:PAINT_protein_info.png|Fig 8]]). You can adjust the relative sizes of each within the window by dragging the line in the partition separating them. Note that the identifier table contains a lot of information that can be observed by scrolling to the right.<br />
<br />
====Navigating withing the Protein Information table====<br />
<br />
* Click anywhere within a row in the table to highlight the protein in the tree and the table.<br />
* Click on one of the blue linkouts will open a link in your web browser.<br />
<br />
<br clear='all'/><br />
----<br />
<br />
===Multiple sequence alignment (MSA)===<br />
[[File:PAINT_msa.png|thumb|450px|Figure 9. Multiple Sequence Alignment view]]<br />
The trees were estimated from an MSA, which can be accessed by clicking the "MSA" button on the right panel. The default view shows the entire alignment ([[Media:PAINT_msa.png|Figure 9]]). The evolutionarily conserved part of the alignment is indicated with uppercase letters. The other less conserved region is in lowercase letters. If a sequence misses a position in the matchstate, it is called a delete state and is designated by a ''dash''. If a sequence needs to insert a position in the less conserved region in order to keep the match state region aligned, it is called an insert state and is designated by a ''dot''.<br />
<br />
The conserved columns are colored with dark blue, blue or light blue, which indicates the conservation of 80%, 60% or 40%, respectively, in the column.<br />
<br />
[[File:PAINT_MSA_domain.png|thumb|450px|Figure 10. View domains in the Multiple Sequence Alignment view]]<br />
<br />
The MSA panel can also display the following two types of data:<br />
<br />
*'''Pfam domains''' The Pfam domain data are overlaid to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Domain ([[Media:PAINT_MSA_domain.png|Figure 10]]). The domains are shown as colored bars. Mouse-over the domain bar to display a brief summary of the domain information. <br />
<br />
[[File:PAINT_MSA_key_residue.png|thumb|450px|Figure 11. View active sites in the Multiple Sequence Alignment view]]<br />
<br />
*'''Active sites''' Active site data were gathered from the UniProt and mapped to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Key Residue ([[Media:PAINT_MSA_key_residue.png|Figure 11]]). Any sequence with active site information will be displayed in bold face. Mouse over the amino acid to view active site information. Coloring is as follows:<br />
**Active site – black<br />
**Binding – Red<br />
**Metal – Orange<br />
**Multiple residue types – Magenta<br />
<br />
<br />
Toggle back and forth between the table view (“Protein Information”) and the MSA view (“MSA”) using the buttons above the table/MSA panel.<br />
<br />
Note: You can view the sequence of a hypothetical ancestral protein (node) by first collapsing the appropriate node.<br />
<br clear='all'/><br />
----<br />
<br />
===Annotations and Evidence windows===<br />
[[File:PAINT_annotation_panel.png|thumb|700px|Figure 12. The annotations window]]<br />
[[File:PAINT_evidence.jpg|thumb|400px|Figure 13. Evidence window]]<br />
To view the annotations associated with a specific protein, click on that protein in the tree or table. Annotations appear in the <code>Annotation pane</code> ([[Media:PAINT_annotation_panel.png|Fig 12]]), containing the following information:<br />
* '''ECO (Evidence code):''' The type evidence code supporting the annotation. <br />
* '''Term name:''' The GO term name and accession. Clicking on the term links out to [http://amigo.geneontology.org/amigo AmiGO]. A term with a NOT annotation is displayed as strikethrough text. <br />
* '''Reference:''' The reference supporting the annotation. Clicking on the reference links out to PubMed. IBA annotations display an internal reference, PAINT_REF:00nnnnn, where nnnnn is the numerical part of the Panther family ID. <br />
* '''With:''' This column contains the evidence to support the inference. <br />
* '''Qualifiers:''' The qualifiers 'NOT', 'colocalizes_with' and 'contributes_to' each have a column in the annotation table, and a checkbox that is checked when the qualifier is present.<br />
* '''Delete:''' This is used to remove an inference made by PAINT (see [[PAINT_User_Guide#Removing_an_IBD_annotation|Removing an IBD annotation section]] below).<br />
<br />
===Evidence window===<br />
<br />
The evidence window ([[Media:PAINT_evidence.jpg|Fig 13]]) displayed automatically generated logs of the tree curation, such as annotations, validation and changes made by the PAINT pipeline upon data release.<br />
<br />
----<br />
<br />
===Curator notes===<br />
<br />
The <code>Curator notes</code> is a text editor used to record notes on the curation process. <code>Curator notes</code> can be modified by going to the <code>File</code> > <code>Update comment</code> menu.<br />
'''NOTE: The purpose of the annotation notes is to convey important points about the annotations and the phylogenetic tree both to other annotators and to users''', so annotators should try to make the notes as clear as possible. <br />
<br />
The annotator may use the Curator notes to describe important points in the annotation process, including: <br />
* References used to annotate the family (for example, a few major reviews)<br />
* Any important points about the family topology, including potential inconsistencies in the tree<br />
* Reasons for annotating to a different node than the MRCA (most common recent ancestor), ie the node that triangulation of annotation identifies. <br />
* Link to GitHub tickets leading to review of the tree annotation.<br />
<br />
----<br />
==PAINT navigation functionality==<br />
<br />
===“Find” function===<br />
[[File:PAINT_Find.jpg|thumb|400px|Figure 14. PAINT 'Find' functionality]]<br />
The Find function (<code>Edit</code> > <code>Find…</code>, Fig 14A) allows you to search for either a gene or a GO term. Select a gene or term search using the radio buttons (Fig 14B). Searches are case-insensitive.<br />
<br />
A gene search matches against exact match of any text stored in the database, such as any sequence identifiers, gene symbol, or even gene name (red arrow, Fig 14C). The search does not return partial match (blue arrow, (Fig 14C). To do a partial match, wildcard character(s) (*) can be added before and/or after the search term. Scroll through the list of matches and click on a specific match to highlight it in the tree, table, and annotation matrix, and to display its annotations in the Annotations window.<br />
<br />
You may search GO terms using text, or you may use numbers to search for GO IDs.<br />
<br clear='all'/><br />
----<br />
<br />
==Making an inference: Transferring annotations==<br />
Ancestral nodes in the tree can be annotated with any GO term that has been experimentally annotated to one (or more) of its descendants. These “inferred” annotations can be propagated to its other descendants.<br />
===Annotating an ancestral node, and propagating to descendants by inheritance===<br />
[[File:Fig13 triangulation.jpg|thumb|450px|Figure 15A. PTHR43114 before annotation]]<br />
<br />
* In the example shown in Fig 15A, 5 proteins are annotated by EXP to the GO term <code>adenine deaminase activity</code> (green squares in the 1st column of the Annotation Matrix, indicated by the red downward arrow). <br />
<br />
'''Tip:''' To view the last common ancestor that can be annotated based on triangulation(*), right click on a GO term, or anywhere in the column that contains that GO term. An inferred node, as well as its descendants, will be highlighted in grey (blue arrow, Fig 15A). <br />
* (*) '''Triangulation''' is the calculation of the last common ancestor of two sequences; in this case PAINT calculates the last common ancestor supporting an annotation to the same GO term. <br />
* Note that the node calculated by triangulation may not be the best on to annotate: the curator can decide to annotate to an more ancient or a more recent ancestor, dependent on other evidence. For example, annotations in other GO aspects may support an earlier annotation than suggested by the triangulation.<br />
* The curator should not assume that the genes in the tree are fully curated with repsect to the primary literature. It may be useful to review other papers, including reviews, to ensure annotations found in the tree accurately represents the current state of knowledge. <br />
<br />
====To annotate an ancestral node====<br />
[[File:Fig15B.jpg|thumb|450px|Figure 15B. PTHR43114 after annotation]]<br />
# Click a GO term (green square) from the Annotation Matrix (Fig. 15B) (or anywhere in the column containing the GO term).<br />
# Drag the term to the ancestral node you wish to annotate. This can be the inferred node or any other nodes. When you mouse over it, a <code>+ sign</code> will be visible next to the node. Release the mouse button to annotate. Click here for a video demo of the procedure: http://youtu.be/8kHrdiuNfos.<br />
# The node is now annotated with that term using the evidence code “IBD” (“Inferred from Biological Descendant”) (Fig. 15B).<br />
# PAINT then automatically propagates the IBD annotation to all descendants of the PAINTEed node, such that all descendants of the node will now be annotated with that term using the evidence code “IBA” (“Inferred from Biological Ancestor”). (Proteins and nodes already annotated with the term or one of its descendant terms will remain unchanged.)<br />
<br />
====Annotating an ancestral node with a qualifier====<br />
[[File:Propagating qualifiers.jpg|thumb|800px|Figure 16. Propagating qualifiers]]<br />
* If you propagate an experimental annotation that has a qualifier, ie. "NOT", "contributes_to" (for MF annotations), or "colocalizes_with" (for CC annotations), the qualifier will also get propagated, unless there are contradictory annotations, ie, annotations ''with'' and annotations ''without'' the qualifier (for the same or for different genes). In that case, a pop-up window will appear to specify whether the annotations with or without the qualifier(s) should be propagated. Click the appropriate radio button, and click on the <code>Continue</code> box to apply the selection (Fig 16).<br />
<br />
=====Notes=====<br />
* You may only annotate a node with a given GO term if '''at least one descendant''' has an annotation to that term or a child term. If you try to propagate a term with no supporting annotation, the node will turn red, and the propagation cannot be made.<br />
* Effectively, the PAINT curator only makes IBD annotations; IBA annotations are generated automatically to all descendants of the node to which an IBD annotation is made.<br />
* The IBD annotation automatically includes evidence for each of the sequences having an EXP annotation to the term or one if its descendants; it is not necessary to propagate individual EXP to generate the evidence for the annotation.<br />
<br />
===Negation of annotations: "NOT" statements===<br />
Background: Since PAINT is a model of the family's evolution, adding a NOT modifier to a descendant (either another node or a leaf) represents a loss of function during evolution, that is, we are stating that the specified function was present in an ancestral protein and has been ''lost'' in the indicated protein or clade. This is a special case of the GO guidelines for NOT, which state that a NOT annotation may be made in situations where a particular function may be expected but is absent.<br />
<br />
PAINT defines two reasons for an evolutionary loss of function, described with two separate evidence codes (ECO): <br />
* IRD = '''I'''nferred from '''R'''apid '''D'''ivergence from ancestral sequence evidence used in manual assertion: Used when there is a long branch, often following a duplication, and significant sequence divergence. For very divergent sequences, predictions are less reliable, even in the presence of a common ancestor. <br />
* IKR = '''I'''nferred from phylogenetic determination of loss of '''K'''ey '''R'''esidues evidence: Used when a residue known to be required for the activity of the protein has mutated. <br />
<br />
In both cases, the node (intermediate or leaf) on which the NOT annotation is placed gets the evidence code selected (IKR or IRD), and descendants, if any, are annotated with the IBA evidence. <br />
<br />
====To add the NOT qualifier to IBD annotations====<br />
[[File:Fig15A.jpg|thumb|450px|Figure 17A. Tree annotated with an IBD]]<br />
[[File:Fig15B.jpg|thumb|450px|Figure 17B. Pop up window to select NOT evidence]]<br />
# From a tree annotated with a IBD annotation (Fig 17A), select a node or protein to be negated. This may be either a directly annotated node or one of its children.<br />
# Click the checkbox in the NOT column of the Annotations window. <br />
# A popup menu will appear (Fig 17B). In the menu <code>Select evidence code for NOT annotation</code>, select one of the radio buttons: <br />
#* NOT due to rapid divergence<br />
#* NOT due to change in key residue(s)<br />
# '''Optional:''' In the box labeled <code>Please enter PMID and select sequence(s) from descendants providing evidence</code>, you may enter data not captured by primary annotation that support the negation. For example if a paper shows that one of the descendants does not have an activity, you can enter the PMID and select which gene was <br />
# '''Optional:''' If appropriate, you may select from the list under <code>Annotate to an ancestor term?</code>, a more general GO term to propagate to the node or sequence instead of the term negated.<br />
* In addition to the annotation no longer propagating downward, a small hash mark will appear near the node in the tree to indicate that the block exists (visible in Fig 15C). Note that a hash mark only indicates the existence of at least one NOT annotation, not that every annotation through that node is negated.<br />
<br />
'''Annotations propagated:'''<br />
[[File:Fig15C.jpg|thumb|450px|Figure 17C. Intermediate node annotated with NOT by IRK. Descendants are annotated with a NOT qualifier and IBA evidence]]<br />
[[File:Fig15D.jpg|thumb|450px|Figure 17D. Leaf node annotated with NOT by IRK.]]<br />
* If the NOT is on a node with descendants, the node will get the evidence code select (IKR or IBD), and the descendants will get an IBA evidence (Fig 17C). <br />
* If the NOT is on a leaf node it will get the evidence code select (IKR or IBD) (Fig 17D).<br />
* Upon export of PAINT annotations:<br />
** Annotations with IKR and all NOT annotations to proteins descended from that node will have the NOT qualifier added (as these have good evidence for loss of function).<br />
** Annotations with IRD and all NOT annotations to proteins descended from that node, no annotation will be exported. Thus this acts like a STOP PROPAGATION.<br />
<br />
==Removing IBD, IKR and IRD annotations==<br />
# Click on the desired node. Nodes with inferred annotations are colored orange.<br />
# Go to the Annotation tab and click the <code>Delete</code> in the Delete column (shown in a red square in Fig 13B).<br />
<br />
'''Notes:'''<br />
* Annotations and qualifiers can only be removed from the specific node to which they were made.<br />
* Primary annotations may be be changed; they may be disputed in the [https://github.com/geneontology/go-annotation/issues GO GitHub go-annotation repo].<br />
<br />
== Partial annotation of trees ==<br />
<br />
<br />
[[File:PTHR24073-RabFamily.jpg|thumb|500px|Figure 18. The RAB GTPase superfamily]]]<br />
<br />
<br />
When you want to annotate a very large family, e.g. the RAB GTPase superfamily (PTHR24073) (Fig 18), it may not be feasible to annotate all clades at the same time. In this kind of situation, you may choose to annotate only the clades you are knowledgeable and confident of, and leave other clades unexamined. When you do this, you should fully annotate the clades you choose to annotate. For example, if you choose to do the IFT27 clade, do it fully. Please don't do piecemeal annotations in various locations that may make it hard for a subsequent annotator to understand what has been done. <br />
<br />
We also agreed at the July 2014 PAINT Jamboree that you can make propagations all the way to the root if you feel that there is an ancestral role, even if you think that some clades have lost this. For example, in the RAB GTPase superfamily, we think that it had an ancestral function as a GTPase, but it is possible that some clades, e.g. the IFT22 clade, have lost this ancestral activity. You can make these high level propagations as part of your initial annotation of the family. If there are clades where this is wrong, perhaps the IBA annotation from PAINT will generate feedback that will help us correct it.<br />
<br />
=== Recording partial annotation in the notes file ===<br />
If you only partially annotate a tree, please record in the notes file which clades you have worked on using the node number, e.g. '''Eukaryota_PTN001180007''' as well as a common name, e.g. '''IFT27''', if it is helpful.<br />
<br />
==Recording trees examined, but not annotated==<br />
<br />
When you examine a tree and feel that it should not be annotated for some reason, please record that in the Evidence Notes so that we can track the fact that the family has been examined. Please use one of these tags (in all caps) in the Notes section of the Evidence tab. You can additional information after the tag if you wish (syntax between tag and additional info not discussed or determined). Then, save your annotations as normal so that PAINT will save the notes file.<br />
<br />
* '''MISSING ANNOTATION''' - Use this if the tree looks OK, but there are insufficient experimental annotations to propagate any annotations.<br />
* '''MISSING SEQUENCE''' - Use this if you feel that a specific sequence or sequences is missing. You can list the IDs of the sequence(s) after the tag.<br />
* '''BAD TREE''' - Use this if you feel that the tree has major problems beyond one or a few missing sequences.<br />
<br />
----<br />
=Interpreting the PANTHER trees=<br />
==Speciation and duplication events, and horizontal transfer==<br />
In the tree, a speciation node is shown with a circle, and a gene duplication node with an square. Horizontal transfer events also appear in the tree, though more rarely, and these are represented with a diamond.<br />
<br />
==Branch lengths==<br />
* Branch lengths show the amount of sequence divergence that has occurred between a given node and its ancestral node, in terms of the average number of amino acid substitutions per site. Shorter branches indicate less sequence divergence and therefore greater conservation of ancestral characters. A branch might be shorter because of a slower evolutionary rate (greater negative selection), or because less "time" has gone by (actually a combination of number of generations and population dynamics), or both.<br />
* Very long branches indicate an unreliable divergence estimate, due to insufficient data. Note that sometimes there is not enough data to compare all branches that descend from a given node. In this case, we have set all descendant branches to a length of 2.0 (very long branches). Branch lengths of 2.0 are often due to a sequence fragment, and at a duplication node it may also indicate a gene that has been incorrectly broken into two different genes by a gene prediction program.<br />
* Following a gene duplication (after a square node), the relative branch lengths for descendant branches are particularly useful: the shortest branch (least diverged) is more likely to have greater functional conservation.<br />
<br />
==Multiple sequence alignment (MSA)==<br />
* Some columns in the MSA have upper-case characters (and dashes '-' for insertions/deletions). These columns were used to estimate the phylogenetic tree.<br />
* Lower-case characters and periods (‘.’ for insertions/deletions) denote positions that were ignored when estimating the phylogenetic tree. Sometimes, tree errors arise because not enough columns were used, and the phylogeny could not be reconstructed well based on the included columns. Since they were not used in the phylogeny, lower-case characters can be particularly helpful in verifying the tree topology: any conserved insertions should be parsimoniously traceable to a common ancestor.<br />
<br />
----<br />
=Reporting bugs or likely errors in the trees=<br />
<br />
==Tree issues==<br />
Most often, the errors in phylogenetic trees are due to problems with the sequence alignment, or the specific MSA columns used to estimate the phylogeny. The phylogeny inference program performs fairly robust handling of sequence fragments, but sequence fragments still cause errors. Another source of error is when the sequences evolve very slowly, generating little variation from which to estimate phylogeny. In this case, the errors can usually be fixed by including additional alignment positions to consider in the phylogeny. <br />
<br />
'''If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues'''<br />
<br />
==PAINT issues==<br />
'''Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues'''<br />
<br />
=Curation Guidelines=<br />
<br />
'''Those guidelines have been published (Gaudet, Livestone, Lewis, Thomas, 2011) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059/?tool=pubmed]'''<br />
<br />
<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2021-07-01<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_User_Guide&diff=86147PAINT User Guide2023-10-17T20:56:40Z<p>Mi: /* Step 1: Find and "lock" families for curation */</p>
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<div><br />
=PAINT Overview=<br />
= PAINT (Phylogenetic Annotation and INference Tool) =<br />
PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO [[Phylogenetic Annotation Project]] to support inference of GO function terms (molecular function, cellular component and biological process) by homology.<br />
== Principles underlying PAINT ==<br />
Annotation of a gene's function by homology is often referred to as "transitive annotation", in which an experimentally-characterized function of one gene is "transferred" to another gene because of their similarity in sequence. This pairwise transfer paradigm derives from the success of sequence searching algorithms such as BLAST and Smith-Waterman. Of course, pairwise conservation of function is really due to descent from a common ancestor (homology). In other words, two sequences of sufficient length are similar because they share a common ancestor, and the reason they have a common function is most likely that they inherited that function from their common ancestor. This process can be explicitly captured using a phylogenetic model.<br />
<br />
Rather than a pairwise paradigm, PAINT uses this more accurate phylogenetic model to infer gene function by homology. PAINT annotation is intended to capture actual inferences about the evolution of gene function within a gene family: the gain, inheritance, modification and loss of function over evolutionary time. Inference is a two-step process, and involves directly annotating a phylogenetic tree. In the first step, experimental GO annotations for extant sequences are used to make inferences about when a given function may have first evolved. In PAINT, this is referred to as "up-propagation", in which ancestral genes are annotated based on information about extant sequences. In the second step, "down-propagation", ancestral annotations are used to make inferences about unannotated extant sequences, based on the principle of inheritance from the common ancestor, and allowing for modification and even loss of function during evolution.<br />
<br />
'''For a more complete description, please see the [[PAINT annotation guidelines]] and the publication on the GO Phylogenetic Annotation process, [https://www.ncbi.nlm.nih.gov/pubmed/21873635 Gaudet et al, Briefings in Bioinformatics, 2011]. '''<br />
<br />
= PAINT software =<br />
PAINT is implemented in Java by Paul Thomas's group (USC). Development of PAINT has been funded by grant GM081084 from the U.S. National Institutes of Health, and the GO Consortium grant 5U41HG002273.<br />
<br />
Software details are available in https://github.com/pantherdb/db-PAINT. Refer to https://github.com/pantherdb/db-PAINT/blob/master/README.md for implementation details.<br />
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== Availability ==<br />
PAINT is freely available for download from the Panther website: https://go.paint.usc.edu/<br />
<br />
==Requirements==<br />
Java 1.8 (aka Java 8 on a Macintosh) must be installed.<br />
<br />
==Installing and configuring PAINT==<br />
PAINT is a Java application, and can be run on a either Mac or Windows. To install PAINT, download the application from: https://go.paint.usc.edu/<br />
<br />
The detailed instruction on installing and configuring the software can be found at https://go.paint.usc.edu/doc/Installation.jsp.<br />
<br />
The entire process to install the software should take no more than 10 minutes.<br />
<br />
== Data versioning ==<br />
* Phylogenetic trees are generated for [http://pantherdb.org PANTHER version 17], released on 2022-02-23.<br />
* The GO ontology version and annotations are updated monthly. <br />
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=Using PAINT=<br />
<br />
==Launching PAINT==<br />
* On a Windows machine, run the program <code>lauchPAINT.bat</code>.<br />
* On a Mac, open a Unix terminal window, go to the directory containing the PAINT program, and execute the command: <br />
<code>sh launchPAINT.sh</code> OR <code>./launchPAINT.sh</code><br />
<br />
==Login==<br />
You are required to login before you can open a tree. The purpose is to record proper acknowledgement for all the curated annotations (of tree nodes) created by you.<br />
<br />
Go to <code>File -> Login</code>.<br />
<br />
If you just want to view the tree and annotations, you can enter <code>gouser</code> as the username. The password is filled already. This is a read-only login. You can only view the tree, but can't lock the family (see below) and curate it.<br />
<br />
If you want to curate trees, enter your username and password. If you don’t have a login and password, send an email to huaiyumi@usc.edu and request one.<br />
<br />
==Curating a gene family==<br />
The analogy is to a library. You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).<br />
<br />
===Step 1: Find and "lock" families for curation===<br />
The "lock" function is only available to a curator's account. If you login to a read-only account, e.g., with "gouser" username, you can't lock a family. You can still search a family and view it.<br />
<br />
When you lock the family, other curators won’t be able to curate them. This is to prevent people from working on the same family.<br />
[[File:PAINT_search.png|thumb|Figure 1. PAINT family search box|450px]]<br />
* Go to <code>File</code> > <code>Manage and View Books...</code><br />
**A window will pop up (Fig 1). <br />
***You can search for families by various identifiers: family ID, ancestral node (PTN) ID, Gene Symbol, Protein Identifier, Gene Identifier, or gene definition. For example, enter PTHR11409 with the "Get Book by ID" option.<br />
***Retrieve a list of all families, or just the uncurated families.<br />
***Retrieve a list of families that require review (incompletely curated).<br />
**Press the "submit" button to launch search<br />
**It normally takes a few seconds to retrieve the results.<br />
[[File:PAINT_family_search_results.png|thumb|Figure 2. PAINT family search results|450px]]<br />
* Select one or several families to lock. Fig 2 shows an example when all uncurated families are returned. There are 4 possible curation status states:<br />
**Manually curated – These are the families curated, and the curator believes that the curation is complete.<br />
**Locked – Those families are locked by a curator. The name of the curator who locks the family is shown in the Locked by column. <br />
**Partially curated – These are the families that have been curated. The curator can unlock the family and leave it as partially curated.<br />
**Require PAINT review – The previously curated paint annotations are changed due to updates in either PANTHER and GO.<br />
**Unknown – These are uncurated families.<br />
*Check the box in the <code>Lock/Unlock</code> column of the families you want to check out, and click <code>Lock or Unlock selected Books</code> button at the bottom of the panel.<br />
<br />
===Step 2: Open a family to curate===<br />
* To open a family, click <code>View Locked Books</code>, and then click the <code>View</code> button (Fig 3). If you login a read-only account, you can click the <code>View</code> button as shown in Fig 2.<br />
* A family can only be locked by a single user. If a family is already locked, you can open it in View Only mode.<br />
* You can only curate families you have locked.<br />
<br />
[[File:PAINT_family_opening.png|thumb|Figure 3. Opening a previously locked family.|450px]]<br />
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===Step 3: Save your annotations===<br />
You can choose to save but keep the family locked so you can continue the curation later. You can also save and unlock the family. <br />
* Go to <code>File</code> > <code>Save to Database</code>. A window will pop up with the following options:<br />
**'''Cancel'''<br />
**'''Save and unlock:''' The family will be unlocked and marked as Partially Curated.<br />
**'''Save:''' The family will remain locked. The curator should do this as often as possible during the curation.<br />
**'''Save, unlock & set curated:''' The family will be marked as Manually Curated.<br />
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<br />
==Appearance and Basic Operation==<br />
===Windows===<br />
PAINT is organized into three main panels (Fig 4): <br />
[[File:PAINT-overview.png|thumb|Figure 4. Main PAINT window|500px]]<br />
* The '''upper left panel''' shows a '''[[PAINT_User_Guide#Phylogenetic_Tree |phylogenetic tree]]'''. <br />
<br />
* The '''upper right panel''' allows you to switch back and forth between (i) the '''[[PAINT_User_Guide#Annotation_matrix |Annotation Matrix]]'''; (ii) the '''[[PAINT_User_Guide#Protein_Information_table |Protein Information Table]]''' and (iii) a multiple sequence alignment '''([[PAINT_User_Guide#Multiple_sequence_alignment_.28MSA.29 |MSA]])''' of all sequences. <br />
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* The '''bottom panel''' contains two tabs: '''[[PAINT_User_Guide#Annotations_window |Annotations]]''' and '''[[PAINT_User_Guide#Evidence_window |Evidence]]'''. <br />
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All the tabbed panes may be resized or split out into windows.<br />
<br />
* Click on a tab (e.g., Protein Information, Evidence) to bring it to the front. <br />
* Click the icons in the tabs or the upper right corner to Undock/Dock, Minimize, Maximize, or close individual tabs or groups of tabs. <br />
* Tabs and panes may also be rearranged within a window by dragging. <br />
* Columns in the Protein Information Table can be resized.<br />
* Windows may be closed, arranged, or resized by dragging boundaries.<br />
<br />
===Recommended configuration for curation===<br />
* Bigger is better. Use as much of the monitor as you can afford. If you are using a laptop, you may wish to attach an external monitor.<br />
* Adjust the width of the window and the partition between the Tree and the Table until you are comfortable with them.<br />
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<br />
===Phylogenetic Tree===<br />
<br />
A phylogenetic tree contains nodes and branches (Fig 5). There are three types of nodes, root, internal and leaf. Leaf nodes correspond to the proteins in the tree. Root and internal nodes represent the inferred most common ancestor of the descendants. Branch length may be interpreted as time estimates between the nodes. <br />
<br />
[[File:Figure 2.png|thumb|Figure 5. PAINT phylogenetic tree|400px]]<br />
The root and internal nodes of the tree are shown as circles (speciation events) and squares (gene duplication events). If the tree has been previously curated, the nodes maybe colored in indicate the type of annotation (e.g., with inferred or experimental evidence). More details will be described in the "Making an inferrence" section of this guide. The nodes have unique identifiers that start with PTN (=PaNther Node), followed by 9 digits. Mouse over a node to see its identifier. If you right-click on a node, a menu will appear with the options to: <br />
* '''Collapse node:''' - the entire clade is collapsed to a single node (rectangle). All the descendants are hidden, but the GO term assignments to them are still available for annotation. Right-click the node again and select "Expand node" to re-expand it. <br />
* '''Reroot to node:''' - make the selected node and the root, and hide the rest of the tree. This is useful when the tree is too large. To bring back the entire tree again, use menu "Tree -> Reset Root to Main". <br />
* '''Export seq ids from leaves:''' the ids of all leave sequences descended from the node are exported to a text file<br />
* '''Prune:''' All nodes descended from the node are removed from the tree.<br />
<br />
The tree branches can be rescaled if they are too long for comfortable viewing or too short to distinguish individual nodes. The default branch scale is 50, which works for most trees. To rescale, select <code>Tree->Scale...</code> and enter a different number. <br />
<br />
====Navigating within the tree====<br />
* Click on a protein name in the tree to highlight the protein in the tree and the table. <br />
* Left-click on a node in the tree to highlight the entire clade descended from it.<br />
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===Annotation matrix===<br />
'''Note: The colors refer to the default colors in PAINT'''<br />
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[[File:PAINT_main.png|thumb|Figure 6. Main PAINT window|500px]]<br />
<br />
The matrix has a row for each gene/gene product in the tree, and a column for each GO term that is directly annotated to at least one gene/gene product in the tree. The annotation matrix gives an overview of the annotations associated with any proteins in table format. It displays one of the three Gene Ontologies at a time. You can switch to a different ontology by clicking the radio button on the upper left part of the window (red arrow, Fig 6). Mouse-over the downward triangle to see the GO term (yellow circle). The terms in the annotation matrix are grouped, with the most specific terms on the left. A few very broad terms such as “protein binding” are not shown, even though they are listed in the Annotations pane.<br />
<br />
Proteins with experimental annotations (IDA, EXP, IMP, IGI, IPI, or IEP evidence codes) for a particular ontology are colored and shown in boldface (blue circles). You may select one ontology at a time to examine using the radio buttons (red arrow) at the top of the window. <br />
<br />
* Click on a protein in the tree and the corresponding row will be highlighted in the matrix. <br />
<br />
[[File:annotation_matrix_color.png|thumb|500px|Figure 7. PAINT Annotation matrix]]<br />
<br />
* The annotations of the corresponding proteins and GO terms in the matrix are shown in colored squares (Fig 7).<br />
** When you first open a tree, only the experimental annotations are shown. These are the annotations than can be used for annotating ancestral genes.<br />
*** Experimental annotations are represented by green color. If it is a direct annotation (i.e. the actual annotation is to that exact term in that column of the matrix), there is a black dot in the middle of the green square. If it is an indirect annotation (i.e. the actual annotation is to a child of the term in that column of the matrix), there is a white dot in the middle of the square.<br />
*** NOT annotations are indicated with by a red circle with a white X.<br />
** When you have annotated an ancestral node, inferred annotations are also shown in the matrix. This allows you to easily keep track of what you've already annotated.<br />
*** Inferred annotations are represented by blue color, with either a black (direct) or white (indirect) dot in the center, or X for NOT as above. <br />
<br />
* Mouse-over an annotation square to see the tool tip of the protein name and the term.<br />
* Click on the annotation square to highlight the row. All the annotations to the protein, as well as the evidences and confidence codes will be displayed in the Annotation panel (see below for more details).<br />
* Right-click (or Command-click in Mac) on the experimental annotation (green square) in the matrix will automatically highlight the inferred most recent common ancestor (MRCA) node for the term.<br />
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===Protein Information table===<br />
[[File:PAINT_protein_info.png|thumb|450px|Figure 8. Protein information table]]<br />
The phylogenetic tree is aligned with a protein information table showing additional information and linkouts to various databases ([[Media:PAINT_protein_info.png|Fig 8]]). You can adjust the relative sizes of each within the window by dragging the line in the partition separating them. Note that the identifier table contains a lot of information that can be observed by scrolling to the right.<br />
<br />
====Navigating withing the Protein Information table====<br />
<br />
* Click anywhere within a row in the table to highlight the protein in the tree and the table.<br />
* Click on one of the blue linkouts will open a link in your web browser.<br />
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===Multiple sequence alignment (MSA)===<br />
[[File:PAINT_msa.png|thumb|450px|Figure 9. Multiple Sequence Alignment view]]<br />
The trees were estimated from an MSA, which can be accessed by clicking the "MSA" button on the right panel. The default view shows the entire alignment ([[Media:PAINT_msa.png|Figure 9]]). The evolutionarily conserved part of the alignment is indicated with uppercase letters. The other less conserved region is in lowercase letters. If a sequence misses a position in the matchstate, it is called a delete state and is designated by a ''dash''. If a sequence needs to insert a position in the less conserved region in order to keep the match state region aligned, it is called an insert state and is designated by a ''dot''.<br />
<br />
The conserved columns are colored with dark blue, blue or light blue, which indicates the conservation of 80%, 60% or 40%, respectively, in the column.<br />
<br />
[[File:PAINT_MSA_domain.png|thumb|450px|Figure 10. View domains in the Multiple Sequence Alignment view]]<br />
<br />
The MSA panel can also display the following two types of data:<br />
<br />
*'''Pfam domains''' The Pfam domain data are overlaid to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Domain ([[Media:PAINT_MSA_domain.png|Figure 10]]). The domains are shown as colored bars. Mouse-over the domain bar to display a brief summary of the domain information. <br />
<br />
[[File:PAINT_MSA_key_residue.png|thumb|450px|Figure 11. View active sites in the Multiple Sequence Alignment view]]<br />
<br />
*'''Active sites''' Active site data were gathered from the UniProt and mapped to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Key Residue ([[Media:PAINT_MSA_key_residue.png|Figure 11]]). Any sequence with active site information will be displayed in bold face. Mouse over the amino acid to view active site information. Coloring is as follows:<br />
**Active site – black<br />
**Binding – Red<br />
**Metal – Orange<br />
**Multiple residue types – Magenta<br />
<br />
<br />
Toggle back and forth between the table view (“Protein Information”) and the MSA view (“MSA”) using the buttons above the table/MSA panel.<br />
<br />
Note: You can view the sequence of a hypothetical ancestral protein (node) by first collapsing the appropriate node.<br />
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===Annotations and Evidence windows===<br />
[[File:PAINT_annotation_panel.png|thumb|700px|Figure 12. The annotations window]]<br />
[[File:PAINT_evidence.jpg|thumb|400px|Figure 13. Evidence window]]<br />
To view the annotations associated with a specific protein, click on that protein in the tree or table. Annotations appear in the <code>Annotation pane</code> ([[Media:PAINT_annotation_panel.png|Fig 12]]), containing the following information:<br />
* '''ECO (Evidence code):''' The type evidence code supporting the annotation. <br />
* '''Term name:''' The GO term name and accession. Clicking on the term links out to [http://amigo.geneontology.org/amigo AmiGO]. A term with a NOT annotation is displayed as strikethrough text. <br />
* '''Reference:''' The reference supporting the annotation. Clicking on the reference links out to PubMed. IBA annotations display an internal reference, PAINT_REF:00nnnnn, where nnnnn is the numerical part of the Panther family ID. <br />
* '''With:''' This column contains the evidence to support the inference. <br />
* '''Qualifiers:''' The qualifiers 'NOT', 'colocalizes_with' and 'contributes_to' each have a column in the annotation table, and a checkbox that is checked when the qualifier is present.<br />
* '''Delete:''' This is used to remove an inference made by PAINT (see [[PAINT_User_Guide#Removing_an_IBD_annotation|Removing an IBD annotation section]] below).<br />
<br />
===Evidence window===<br />
<br />
The evidence window ([[Media:PAINT_evidence.jpg|Fig 13]]) displayed automatically generated logs of the tree curation, such as annotations, validation and changes made by the PAINT pipeline upon data release.<br />
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===Curator notes===<br />
<br />
The <code>Curator notes</code> is a text editor used to record notes on the curation process. <code>Curator notes</code> can be modified by going to the <code>File</code> > <code>Update comment</code> menu.<br />
'''NOTE: The purpose of the annotation notes is to convey important points about the annotations and the phylogenetic tree both to other annotators and to users''', so annotators should try to make the notes as clear as possible. <br />
<br />
The annotator may use the Curator notes to describe important points in the annotation process, including: <br />
* References used to annotate the family (for example, a few major reviews)<br />
* Any important points about the family topology, including potential inconsistencies in the tree<br />
* Reasons for annotating to a different node than the MRCA (most common recent ancestor), ie the node that triangulation of annotation identifies. <br />
* Link to GitHub tickets leading to review of the tree annotation.<br />
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==PAINT navigation functionality==<br />
<br />
===“Find” function===<br />
[[File:PAINT_Find.jpg|thumb|400px|Figure 14. PAINT 'Find' functionality]]<br />
The Find function (<code>Edit</code> > <code>Find…</code>, Fig 14A) allows you to search for either a gene or a GO term. Select a gene or term search using the radio buttons (Fig 14B). Searches are case-insensitive.<br />
<br />
A gene search matches against exact match of any text stored in the database, such as any sequence identifiers, gene symbol, or even gene name (red arrow, Fig 14C). The search does not return partial match (blue arrow, (Fig 14C). To do a partial match, wildcard character(s) (*) can be added before and/or after the search term. Scroll through the list of matches and click on a specific match to highlight it in the tree, table, and annotation matrix, and to display its annotations in the Annotations window.<br />
<br />
You may search GO terms using text, or you may use numbers to search for GO IDs.<br />
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==Making an inference: Transferring annotations==<br />
Ancestral nodes in the tree can be annotated with any GO term that has been experimentally annotated to one (or more) of its descendants. These “inferred” annotations can be propagated to its other descendants.<br />
===Annotating an ancestral node, and propagating to descendants by inheritance===<br />
[[File:Fig13 triangulation.jpg|thumb|450px|Figure 15A. PTHR43114 before annotation]]<br />
<br />
* In the example shown in Fig 15A, 5 proteins are annotated by EXP to the GO term <code>adenine deaminase activity</code> (green squares in the 1st column of the Annotation Matrix, indicated by the red downward arrow). <br />
<br />
'''Tip:''' To view the last common ancestor that can be annotated based on triangulation(*), right click on a GO term, or anywhere in the column that contains that GO term. An inferred node, as well as its descendants, will be highlighted in grey (blue arrow, Fig 15A). <br />
* (*) '''Triangulation''' is the calculation of the last common ancestor of two sequences; in this case PAINT calculates the last common ancestor supporting an annotation to the same GO term. <br />
* Note that the node calculated by triangulation may not be the best on to annotate: the curator can decide to annotate to an more ancient or a more recent ancestor, dependent on other evidence. For example, annotations in other GO aspects may support an earlier annotation than suggested by the triangulation.<br />
* The curator should not assume that the genes in the tree are fully curated with repsect to the primary literature. It may be useful to review other papers, including reviews, to ensure annotations found in the tree accurately represents the current state of knowledge. <br />
<br />
====To annotate an ancestral node====<br />
[[File:Fig15B.jpg|thumb|450px|Figure 15B. PTHR43114 after annotation]]<br />
# Click a GO term (green square) from the Annotation Matrix (Fig. 15B) (or anywhere in the column containing the GO term).<br />
# Drag the term to the ancestral node you wish to annotate. This can be the inferred node or any other nodes. When you mouse over it, a <code>+ sign</code> will be visible next to the node. Release the mouse button to annotate. Click here for a video demo of the procedure: http://youtu.be/8kHrdiuNfos.<br />
# The node is now annotated with that term using the evidence code “IBD” (“Inferred from Biological Descendant”) (Fig. 15B).<br />
# PAINT then automatically propagates the IBD annotation to all descendants of the PAINTEed node, such that all descendants of the node will now be annotated with that term using the evidence code “IBA” (“Inferred from Biological Ancestor”). (Proteins and nodes already annotated with the term or one of its descendant terms will remain unchanged.)<br />
<br />
====Annotating an ancestral node with a qualifier====<br />
[[File:Propagating qualifiers.jpg|thumb|800px|Figure 16. Propagating qualifiers]]<br />
* If you propagate an experimental annotation that has a qualifier, ie. "NOT", "contributes_to" (for MF annotations), or "colocalizes_with" (for CC annotations), the qualifier will also get propagated, unless there are contradictory annotations, ie, annotations ''with'' and annotations ''without'' the qualifier (for the same or for different genes). In that case, a pop-up window will appear to specify whether the annotations with or without the qualifier(s) should be propagated. Click the appropriate radio button, and click on the <code>Continue</code> box to apply the selection (Fig 16).<br />
<br />
=====Notes=====<br />
* You may only annotate a node with a given GO term if '''at least one descendant''' has an annotation to that term or a child term. If you try to propagate a term with no supporting annotation, the node will turn red, and the propagation cannot be made.<br />
* Effectively, the PAINT curator only makes IBD annotations; IBA annotations are generated automatically to all descendants of the node to which an IBD annotation is made.<br />
* The IBD annotation automatically includes evidence for each of the sequences having an EXP annotation to the term or one if its descendants; it is not necessary to propagate individual EXP to generate the evidence for the annotation.<br />
<br />
===Negation of annotations: "NOT" statements===<br />
Background: Since PAINT is a model of the family's evolution, adding a NOT modifier to a descendant (either another node or a leaf) represents a loss of function during evolution, that is, we are stating that the specified function was present in an ancestral protein and has been ''lost'' in the indicated protein or clade. This is a special case of the GO guidelines for NOT, which state that a NOT annotation may be made in situations where a particular function may be expected but is absent.<br />
<br />
PAINT defines two reasons for an evolutionary loss of function, described with two separate evidence codes (ECO): <br />
* IRD = '''I'''nferred from '''R'''apid '''D'''ivergence from ancestral sequence evidence used in manual assertion: Used when there is a long branch, often following a duplication, and significant sequence divergence. For very divergent sequences, predictions are less reliable, even in the presence of a common ancestor. <br />
* IKR = '''I'''nferred from phylogenetic determination of loss of '''K'''ey '''R'''esidues evidence: Used when a residue known to be required for the activity of the protein has mutated. <br />
<br />
In both cases, the node (intermediate or leaf) on which the NOT annotation is placed gets the evidence code selected (IKR or IRD), and descendants, if any, are annotated with the IBA evidence. <br />
<br />
====To add the NOT qualifier to IBD annotations====<br />
[[File:Fig15A.jpg|thumb|450px|Figure 17A. Tree annotated with an IBD]]<br />
[[File:Fig15B.jpg|thumb|450px|Figure 17B. Pop up window to select NOT evidence]]<br />
# From a tree annotated with a IBD annotation (Fig 17A), select a node or protein to be negated. This may be either a directly annotated node or one of its children.<br />
# Click the checkbox in the NOT column of the Annotations window. <br />
# A popup menu will appear (Fig 17B). In the menu <code>Select evidence code for NOT annotation</code>, select one of the radio buttons: <br />
#* NOT due to rapid divergence<br />
#* NOT due to change in key residue(s)<br />
# '''Optional:''' In the box labeled <code>Please enter PMID and select sequence(s) from descendants providing evidence</code>, you may enter data not captured by primary annotation that support the negation. For example if a paper shows that one of the descendants does not have an activity, you can enter the PMID and select which gene was <br />
# '''Optional:''' If appropriate, you may select from the list under <code>Annotate to an ancestor term?</code>, a more general GO term to propagate to the node or sequence instead of the term negated.<br />
* In addition to the annotation no longer propagating downward, a small hash mark will appear near the node in the tree to indicate that the block exists (visible in Fig 15C). Note that a hash mark only indicates the existence of at least one NOT annotation, not that every annotation through that node is negated.<br />
<br />
'''Annotations propagated:'''<br />
[[File:Fig15C.jpg|thumb|450px|Figure 17C. Intermediate node annotated with NOT by IRK. Descendants are annotated with a NOT qualifier and IBA evidence]]<br />
[[File:Fig15D.jpg|thumb|450px|Figure 17D. Leaf node annotated with NOT by IRK.]]<br />
* If the NOT is on a node with descendants, the node will get the evidence code select (IKR or IBD), and the descendants will get an IBA evidence (Fig 17C). <br />
* If the NOT is on a leaf node it will get the evidence code select (IKR or IBD) (Fig 17D).<br />
* Upon export of PAINT annotations:<br />
** Annotations with IKR and all NOT annotations to proteins descended from that node will have the NOT qualifier added (as these have good evidence for loss of function).<br />
** Annotations with IRD and all NOT annotations to proteins descended from that node, no annotation will be exported. Thus this acts like a STOP PROPAGATION.<br />
<br />
==Removing IBD, IKR and IRD annotations==<br />
# Click on the desired node. Nodes with inferred annotations are colored orange.<br />
# Go to the Annotation tab and click the <code>Delete</code> in the Delete column (shown in a red square in Fig 13B).<br />
<br />
'''Notes:'''<br />
* Annotations and qualifiers can only be removed from the specific node to which they were made.<br />
* Primary annotations may be be changed; they may be disputed in the [https://github.com/geneontology/go-annotation/issues GO GitHub go-annotation repo].<br />
<br />
== Partial annotation of trees ==<br />
<br />
<br />
[[File:PTHR24073-RabFamily.jpg|thumb|500px|Figure 18. The RAB GTPase superfamily]]]<br />
<br />
<br />
When you want to annotate a very large family, e.g. the RAB GTPase superfamily (PTHR24073) (Fig 18), it may not be feasible to annotate all clades at the same time. In this kind of situation, you may choose to annotate only the clades you are knowledgeable and confident of, and leave other clades unexamined. When you do this, you should fully annotate the clades you choose to annotate. For example, if you choose to do the IFT27 clade, do it fully. Please don't do piecemeal annotations in various locations that may make it hard for a subsequent annotator to understand what has been done. <br />
<br />
We also agreed at the July 2014 PAINT Jamboree that you can make propagations all the way to the root if you feel that there is an ancestral role, even if you think that some clades have lost this. For example, in the RAB GTPase superfamily, we think that it had an ancestral function as a GTPase, but it is possible that some clades, e.g. the IFT22 clade, have lost this ancestral activity. You can make these high level propagations as part of your initial annotation of the family. If there are clades where this is wrong, perhaps the IBA annotation from PAINT will generate feedback that will help us correct it.<br />
<br />
=== Recording partial annotation in the notes file ===<br />
If you only partially annotate a tree, please record in the notes file which clades you have worked on using the node number, e.g. '''Eukaryota_PTN001180007''' as well as a common name, e.g. '''IFT27''', if it is helpful.<br />
<br />
==Recording trees examined, but not annotated==<br />
<br />
When you examine a tree and feel that it should not be annotated for some reason, please record that in the Evidence Notes so that we can track the fact that the family has been examined. Please use one of these tags (in all caps) in the Notes section of the Evidence tab. You can additional information after the tag if you wish (syntax between tag and additional info not discussed or determined). Then, save your annotations as normal so that PAINT will save the notes file.<br />
<br />
* '''MISSING ANNOTATION''' - Use this if the tree looks OK, but there are insufficient experimental annotations to propagate any annotations.<br />
* '''MISSING SEQUENCE''' - Use this if you feel that a specific sequence or sequences is missing. You can list the IDs of the sequence(s) after the tag.<br />
* '''BAD TREE''' - Use this if you feel that the tree has major problems beyond one or a few missing sequences.<br />
<br />
----<br />
=Interpreting the PANTHER trees=<br />
==Speciation and duplication events, and horizontal transfer==<br />
In the tree, a speciation node is shown with a circle, and a gene duplication node with an square. Horizontal transfer events also appear in the tree, though more rarely, and these are represented with a diamond.<br />
<br />
==Branch lengths==<br />
* Branch lengths show the amount of sequence divergence that has occurred between a given node and its ancestral node, in terms of the average number of amino acid substitutions per site. Shorter branches indicate less sequence divergence and therefore greater conservation of ancestral characters. A branch might be shorter because of a slower evolutionary rate (greater negative selection), or because less "time" has gone by (actually a combination of number of generations and population dynamics), or both.<br />
* Very long branches indicate an unreliable divergence estimate, due to insufficient data. Note that sometimes there is not enough data to compare all branches that descend from a given node. In this case, we have set all descendant branches to a length of 2.0 (very long branches). Branch lengths of 2.0 are often due to a sequence fragment, and at a duplication node it may also indicate a gene that has been incorrectly broken into two different genes by a gene prediction program.<br />
* Following a gene duplication (after a square node), the relative branch lengths for descendant branches are particularly useful: the shortest branch (least diverged) is more likely to have greater functional conservation.<br />
<br />
==Multiple sequence alignment (MSA)==<br />
* Some columns in the MSA have upper-case characters (and dashes '-' for insertions/deletions). These columns were used to estimate the phylogenetic tree.<br />
* Lower-case characters and periods (‘.’ for insertions/deletions) denote positions that were ignored when estimating the phylogenetic tree. Sometimes, tree errors arise because not enough columns were used, and the phylogeny could not be reconstructed well based on the included columns. Since they were not used in the phylogeny, lower-case characters can be particularly helpful in verifying the tree topology: any conserved insertions should be parsimoniously traceable to a common ancestor.<br />
<br />
----<br />
=Reporting bugs or likely errors in the trees=<br />
<br />
==Tree issues==<br />
Most often, the errors in phylogenetic trees are due to problems with the sequence alignment, or the specific MSA columns used to estimate the phylogeny. The phylogeny inference program performs fairly robust handling of sequence fragments, but sequence fragments still cause errors. Another source of error is when the sequences evolve very slowly, generating little variation from which to estimate phylogeny. In this case, the errors can usually be fixed by including additional alignment positions to consider in the phylogeny. <br />
<br />
'''If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues'''<br />
<br />
==PAINT issues==<br />
'''Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues'''<br />
<br />
=Curation Guidelines=<br />
<br />
'''Those guidelines have been published (Gaudet, Livestone, Lewis, Thomas, 2011) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059/?tool=pubmed]'''<br />
<br />
<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2021-07-01<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_User_Guide&diff=86146PAINT User Guide2023-10-17T20:54:25Z<p>Mi: /* Curating a gene family */</p>
<hr />
<div><br />
=PAINT Overview=<br />
= PAINT (Phylogenetic Annotation and INference Tool) =<br />
PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO [[Phylogenetic Annotation Project]] to support inference of GO function terms (molecular function, cellular component and biological process) by homology.<br />
== Principles underlying PAINT ==<br />
Annotation of a gene's function by homology is often referred to as "transitive annotation", in which an experimentally-characterized function of one gene is "transferred" to another gene because of their similarity in sequence. This pairwise transfer paradigm derives from the success of sequence searching algorithms such as BLAST and Smith-Waterman. Of course, pairwise conservation of function is really due to descent from a common ancestor (homology). In other words, two sequences of sufficient length are similar because they share a common ancestor, and the reason they have a common function is most likely that they inherited that function from their common ancestor. This process can be explicitly captured using a phylogenetic model.<br />
<br />
Rather than a pairwise paradigm, PAINT uses this more accurate phylogenetic model to infer gene function by homology. PAINT annotation is intended to capture actual inferences about the evolution of gene function within a gene family: the gain, inheritance, modification and loss of function over evolutionary time. Inference is a two-step process, and involves directly annotating a phylogenetic tree. In the first step, experimental GO annotations for extant sequences are used to make inferences about when a given function may have first evolved. In PAINT, this is referred to as "up-propagation", in which ancestral genes are annotated based on information about extant sequences. In the second step, "down-propagation", ancestral annotations are used to make inferences about unannotated extant sequences, based on the principle of inheritance from the common ancestor, and allowing for modification and even loss of function during evolution.<br />
<br />
'''For a more complete description, please see the [[PAINT annotation guidelines]] and the publication on the GO Phylogenetic Annotation process, [https://www.ncbi.nlm.nih.gov/pubmed/21873635 Gaudet et al, Briefings in Bioinformatics, 2011]. '''<br />
<br />
= PAINT software =<br />
PAINT is implemented in Java by Paul Thomas's group (USC). Development of PAINT has been funded by grant GM081084 from the U.S. National Institutes of Health, and the GO Consortium grant 5U41HG002273.<br />
<br />
Software details are available in https://github.com/pantherdb/db-PAINT. Refer to https://github.com/pantherdb/db-PAINT/blob/master/README.md for implementation details.<br />
<br />
== Availability ==<br />
PAINT is freely available for download from the Panther website: https://go.paint.usc.edu/<br />
<br />
==Requirements==<br />
Java 1.8 (aka Java 8 on a Macintosh) must be installed.<br />
<br />
==Installing and configuring PAINT==<br />
PAINT is a Java application, and can be run on a either Mac or Windows. To install PAINT, download the application from: https://go.paint.usc.edu/<br />
<br />
The detailed instruction on installing and configuring the software can be found at https://go.paint.usc.edu/doc/Installation.jsp.<br />
<br />
The entire process to install the software should take no more than 10 minutes.<br />
<br />
== Data versioning ==<br />
* Phylogenetic trees are generated for [http://pantherdb.org PANTHER version 17], released on 2022-02-23.<br />
* The GO ontology version and annotations are updated monthly. <br />
<br />
----<br />
<br />
=Using PAINT=<br />
<br />
==Launching PAINT==<br />
* On a Windows machine, run the program <code>lauchPAINT.bat</code>.<br />
* On a Mac, open a Unix terminal window, go to the directory containing the PAINT program, and execute the command: <br />
<code>sh launchPAINT.sh</code> OR <code>./launchPAINT.sh</code><br />
<br />
==Login==<br />
You are required to login before you can open a tree. The purpose is to record proper acknowledgement for all the curated annotations (of tree nodes) created by you.<br />
<br />
Go to <code>File -> Login</code>.<br />
<br />
If you just want to view the tree and annotations, you can enter <code>gouser</code> as the username. The password is filled already. This is a read-only login. You can only view the tree, but can't lock the family (see below) and curate it.<br />
<br />
If you want to curate trees, enter your username and password. If you don’t have a login and password, send an email to huaiyumi@usc.edu and request one.<br />
<br />
==Curating a gene family==<br />
The analogy is to a library. You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).<br />
<br />
===Step 1: Find and "lock" families for curation===<br />
The "lock" function is only available to a curator's account. If you login to a read-only account, e.g., with "gouser" username, you can't lock a family. You can still search a family and view it.<br />
<br />
When you lock the family, other curators won’t be able to curate them. This is to prevent people from working on the same family.<br />
[[File:PAINT_search.png|thumb|Figure 1. PAINT family search box|450px]]<br />
* Go to <code>File</code> > <code>Manage and View Books...</code><br />
**A window will pop up (Fig 1). <br />
***You can search for families by various identifiers: family ID, ancestral node (PTN) ID, Gene Symbol, Protein Identifier, Gene Identifier, or gene definition. For example, enter PTHR11409 with the "Get Book by ID" option.<br />
***Retrieve a list of all families, or just the uncurated families.<br />
***Retrieve a list of families that require review (incompletely curated).<br />
**Press the "submit" button to launch search<br />
[[File:PAINT_family_search_results.png|thumb|Figure 2. PAINT family search results|450px]]<br />
* Select one or several families to lock. Fig 2 shows an example when all uncurated families are returned. There are 4 possible curation status states:<br />
**Manually curated – These are the families curated, and the curator believes that the curation is complete.<br />
**Locked – Those families are locked by a curator. The name of the curator who locks the family is shown in the Locked by column. <br />
**Partially curated – These are the families that have been curated. The curator can unlock the family and leave it as partially curated.<br />
**Require PAINT review – The previously curated paint annotations are changed due to updates in either PANTHER and GO.<br />
**Unknown – These are uncurated families.<br />
*Check the box in the <code>Lock/Unlock</code> column of the families you want to check out, and click <code>Lock or Unlock selected Books</code> button at the bottom of the panel.<br />
<br />
===Step 2: Open a family to curate===<br />
* To open a family, click <code>View Locked Books</code>, and then click the <code>View</code> button (Fig 3). If you login a read-only account, you can click the <code>View</code> button as shown in Fig 2.<br />
* A family can only be locked by a single user. If a family is already locked, you can open it in View Only mode.<br />
* You can only curate families you have locked.<br />
<br />
[[File:PAINT_family_opening.png|thumb|Figure 3. Opening a previously locked family.|450px]]<br />
<br />
===Step 3: Save your annotations===<br />
You can choose to save but keep the family locked so you can continue the curation later. You can also save and unlock the family. <br />
* Go to <code>File</code> > <code>Save to Database</code>. A window will pop up with the following options:<br />
**'''Cancel'''<br />
**'''Save and unlock:''' The family will be unlocked and marked as Partially Curated.<br />
**'''Save:''' The family will remain locked. The curator should do this as often as possible during the curation.<br />
**'''Save, unlock & set curated:''' The family will be marked as Manually Curated.<br />
<br />
----<br />
<br />
==Appearance and Basic Operation==<br />
===Windows===<br />
PAINT is organized into three main panels (Fig 4): <br />
[[File:PAINT-overview.png|thumb|Figure 4. Main PAINT window|500px]]<br />
* The '''upper left panel''' shows a '''[[PAINT_User_Guide#Phylogenetic_Tree |phylogenetic tree]]'''. <br />
<br />
* The '''upper right panel''' allows you to switch back and forth between (i) the '''[[PAINT_User_Guide#Annotation_matrix |Annotation Matrix]]'''; (ii) the '''[[PAINT_User_Guide#Protein_Information_table |Protein Information Table]]''' and (iii) a multiple sequence alignment '''([[PAINT_User_Guide#Multiple_sequence_alignment_.28MSA.29 |MSA]])''' of all sequences. <br />
<br />
* The '''bottom panel''' contains two tabs: '''[[PAINT_User_Guide#Annotations_window |Annotations]]''' and '''[[PAINT_User_Guide#Evidence_window |Evidence]]'''. <br />
<br />
All the tabbed panes may be resized or split out into windows.<br />
<br />
* Click on a tab (e.g., Protein Information, Evidence) to bring it to the front. <br />
* Click the icons in the tabs or the upper right corner to Undock/Dock, Minimize, Maximize, or close individual tabs or groups of tabs. <br />
* Tabs and panes may also be rearranged within a window by dragging. <br />
* Columns in the Protein Information Table can be resized.<br />
* Windows may be closed, arranged, or resized by dragging boundaries.<br />
<br />
===Recommended configuration for curation===<br />
* Bigger is better. Use as much of the monitor as you can afford. If you are using a laptop, you may wish to attach an external monitor.<br />
* Adjust the width of the window and the partition between the Tree and the Table until you are comfortable with them.<br />
<br />
----<br />
<br />
===Phylogenetic Tree===<br />
<br />
A phylogenetic tree contains nodes and branches (Fig 5). There are three types of nodes, root, internal and leaf. Leaf nodes correspond to the proteins in the tree. Root and internal nodes represent the inferred most common ancestor of the descendants. Branch length may be interpreted as time estimates between the nodes. <br />
<br />
[[File:Figure 2.png|thumb|Figure 5. PAINT phylogenetic tree|400px]]<br />
The root and internal nodes of the tree are shown as circles (speciation events) and squares (gene duplication events). If the tree has been previously curated, the nodes maybe colored in indicate the type of annotation (e.g., with inferred or experimental evidence). More details will be described in the "Making an inferrence" section of this guide. The nodes have unique identifiers that start with PTN (=PaNther Node), followed by 9 digits. Mouse over a node to see its identifier. If you right-click on a node, a menu will appear with the options to: <br />
* '''Collapse node:''' - the entire clade is collapsed to a single node (rectangle). All the descendants are hidden, but the GO term assignments to them are still available for annotation. Right-click the node again and select "Expand node" to re-expand it. <br />
* '''Reroot to node:''' - make the selected node and the root, and hide the rest of the tree. This is useful when the tree is too large. To bring back the entire tree again, use menu "Tree -> Reset Root to Main". <br />
* '''Export seq ids from leaves:''' the ids of all leave sequences descended from the node are exported to a text file<br />
* '''Prune:''' All nodes descended from the node are removed from the tree.<br />
<br />
The tree branches can be rescaled if they are too long for comfortable viewing or too short to distinguish individual nodes. The default branch scale is 50, which works for most trees. To rescale, select <code>Tree->Scale...</code> and enter a different number. <br />
<br />
====Navigating within the tree====<br />
* Click on a protein name in the tree to highlight the protein in the tree and the table. <br />
* Left-click on a node in the tree to highlight the entire clade descended from it.<br />
<br />
----<br />
<br />
===Annotation matrix===<br />
'''Note: The colors refer to the default colors in PAINT'''<br />
<br />
[[File:PAINT_main.png|thumb|Figure 6. Main PAINT window|500px]]<br />
<br />
The matrix has a row for each gene/gene product in the tree, and a column for each GO term that is directly annotated to at least one gene/gene product in the tree. The annotation matrix gives an overview of the annotations associated with any proteins in table format. It displays one of the three Gene Ontologies at a time. You can switch to a different ontology by clicking the radio button on the upper left part of the window (red arrow, Fig 6). Mouse-over the downward triangle to see the GO term (yellow circle). The terms in the annotation matrix are grouped, with the most specific terms on the left. A few very broad terms such as “protein binding” are not shown, even though they are listed in the Annotations pane.<br />
<br />
Proteins with experimental annotations (IDA, EXP, IMP, IGI, IPI, or IEP evidence codes) for a particular ontology are colored and shown in boldface (blue circles). You may select one ontology at a time to examine using the radio buttons (red arrow) at the top of the window. <br />
<br />
* Click on a protein in the tree and the corresponding row will be highlighted in the matrix. <br />
<br />
[[File:annotation_matrix_color.png|thumb|500px|Figure 7. PAINT Annotation matrix]]<br />
<br />
* The annotations of the corresponding proteins and GO terms in the matrix are shown in colored squares (Fig 7).<br />
** When you first open a tree, only the experimental annotations are shown. These are the annotations than can be used for annotating ancestral genes.<br />
*** Experimental annotations are represented by green color. If it is a direct annotation (i.e. the actual annotation is to that exact term in that column of the matrix), there is a black dot in the middle of the green square. If it is an indirect annotation (i.e. the actual annotation is to a child of the term in that column of the matrix), there is a white dot in the middle of the square.<br />
*** NOT annotations are indicated with by a red circle with a white X.<br />
** When you have annotated an ancestral node, inferred annotations are also shown in the matrix. This allows you to easily keep track of what you've already annotated.<br />
*** Inferred annotations are represented by blue color, with either a black (direct) or white (indirect) dot in the center, or X for NOT as above. <br />
<br />
* Mouse-over an annotation square to see the tool tip of the protein name and the term.<br />
* Click on the annotation square to highlight the row. All the annotations to the protein, as well as the evidences and confidence codes will be displayed in the Annotation panel (see below for more details).<br />
* Right-click (or Command-click in Mac) on the experimental annotation (green square) in the matrix will automatically highlight the inferred most recent common ancestor (MRCA) node for the term.<br />
<br />
----<br />
<br />
===Protein Information table===<br />
[[File:PAINT_protein_info.png|thumb|450px|Figure 8. Protein information table]]<br />
The phylogenetic tree is aligned with a protein information table showing additional information and linkouts to various databases ([[Media:PAINT_protein_info.png|Fig 8]]). You can adjust the relative sizes of each within the window by dragging the line in the partition separating them. Note that the identifier table contains a lot of information that can be observed by scrolling to the right.<br />
<br />
====Navigating withing the Protein Information table====<br />
<br />
* Click anywhere within a row in the table to highlight the protein in the tree and the table.<br />
* Click on one of the blue linkouts will open a link in your web browser.<br />
<br />
<br clear='all'/><br />
----<br />
<br />
===Multiple sequence alignment (MSA)===<br />
[[File:PAINT_msa.png|thumb|450px|Figure 9. Multiple Sequence Alignment view]]<br />
The trees were estimated from an MSA, which can be accessed by clicking the "MSA" button on the right panel. The default view shows the entire alignment ([[Media:PAINT_msa.png|Figure 9]]). The evolutionarily conserved part of the alignment is indicated with uppercase letters. The other less conserved region is in lowercase letters. If a sequence misses a position in the matchstate, it is called a delete state and is designated by a ''dash''. If a sequence needs to insert a position in the less conserved region in order to keep the match state region aligned, it is called an insert state and is designated by a ''dot''.<br />
<br />
The conserved columns are colored with dark blue, blue or light blue, which indicates the conservation of 80%, 60% or 40%, respectively, in the column.<br />
<br />
[[File:PAINT_MSA_domain.png|thumb|450px|Figure 10. View domains in the Multiple Sequence Alignment view]]<br />
<br />
The MSA panel can also display the following two types of data:<br />
<br />
*'''Pfam domains''' The Pfam domain data are overlaid to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Domain ([[Media:PAINT_MSA_domain.png|Figure 10]]). The domains are shown as colored bars. Mouse-over the domain bar to display a brief summary of the domain information. <br />
<br />
[[File:PAINT_MSA_key_residue.png|thumb|450px|Figure 11. View active sites in the Multiple Sequence Alignment view]]<br />
<br />
*'''Active sites''' Active site data were gathered from the UniProt and mapped to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Key Residue ([[Media:PAINT_MSA_key_residue.png|Figure 11]]). Any sequence with active site information will be displayed in bold face. Mouse over the amino acid to view active site information. Coloring is as follows:<br />
**Active site – black<br />
**Binding – Red<br />
**Metal – Orange<br />
**Multiple residue types – Magenta<br />
<br />
<br />
Toggle back and forth between the table view (“Protein Information”) and the MSA view (“MSA”) using the buttons above the table/MSA panel.<br />
<br />
Note: You can view the sequence of a hypothetical ancestral protein (node) by first collapsing the appropriate node.<br />
<br clear='all'/><br />
----<br />
<br />
===Annotations and Evidence windows===<br />
[[File:PAINT_annotation_panel.png|thumb|700px|Figure 12. The annotations window]]<br />
[[File:PAINT_evidence.jpg|thumb|400px|Figure 13. Evidence window]]<br />
To view the annotations associated with a specific protein, click on that protein in the tree or table. Annotations appear in the <code>Annotation pane</code> ([[Media:PAINT_annotation_panel.png|Fig 12]]), containing the following information:<br />
* '''ECO (Evidence code):''' The type evidence code supporting the annotation. <br />
* '''Term name:''' The GO term name and accession. Clicking on the term links out to [http://amigo.geneontology.org/amigo AmiGO]. A term with a NOT annotation is displayed as strikethrough text. <br />
* '''Reference:''' The reference supporting the annotation. Clicking on the reference links out to PubMed. IBA annotations display an internal reference, PAINT_REF:00nnnnn, where nnnnn is the numerical part of the Panther family ID. <br />
* '''With:''' This column contains the evidence to support the inference. <br />
* '''Qualifiers:''' The qualifiers 'NOT', 'colocalizes_with' and 'contributes_to' each have a column in the annotation table, and a checkbox that is checked when the qualifier is present.<br />
* '''Delete:''' This is used to remove an inference made by PAINT (see [[PAINT_User_Guide#Removing_an_IBD_annotation|Removing an IBD annotation section]] below).<br />
<br />
===Evidence window===<br />
<br />
The evidence window ([[Media:PAINT_evidence.jpg|Fig 13]]) displayed automatically generated logs of the tree curation, such as annotations, validation and changes made by the PAINT pipeline upon data release.<br />
<br />
----<br />
<br />
===Curator notes===<br />
<br />
The <code>Curator notes</code> is a text editor used to record notes on the curation process. <code>Curator notes</code> can be modified by going to the <code>File</code> > <code>Update comment</code> menu.<br />
'''NOTE: The purpose of the annotation notes is to convey important points about the annotations and the phylogenetic tree both to other annotators and to users''', so annotators should try to make the notes as clear as possible. <br />
<br />
The annotator may use the Curator notes to describe important points in the annotation process, including: <br />
* References used to annotate the family (for example, a few major reviews)<br />
* Any important points about the family topology, including potential inconsistencies in the tree<br />
* Reasons for annotating to a different node than the MRCA (most common recent ancestor), ie the node that triangulation of annotation identifies. <br />
* Link to GitHub tickets leading to review of the tree annotation.<br />
<br />
----<br />
==PAINT navigation functionality==<br />
<br />
===“Find” function===<br />
[[File:PAINT_Find.jpg|thumb|400px|Figure 14. PAINT 'Find' functionality]]<br />
The Find function (<code>Edit</code> > <code>Find…</code>, Fig 14A) allows you to search for either a gene or a GO term. Select a gene or term search using the radio buttons (Fig 14B). Searches are case-insensitive.<br />
<br />
A gene search matches against exact match of any text stored in the database, such as any sequence identifiers, gene symbol, or even gene name (red arrow, Fig 14C). The search does not return partial match (blue arrow, (Fig 14C). To do a partial match, wildcard character(s) (*) can be added before and/or after the search term. Scroll through the list of matches and click on a specific match to highlight it in the tree, table, and annotation matrix, and to display its annotations in the Annotations window.<br />
<br />
You may search GO terms using text, or you may use numbers to search for GO IDs.<br />
<br clear='all'/><br />
----<br />
<br />
==Making an inference: Transferring annotations==<br />
Ancestral nodes in the tree can be annotated with any GO term that has been experimentally annotated to one (or more) of its descendants. These “inferred” annotations can be propagated to its other descendants.<br />
===Annotating an ancestral node, and propagating to descendants by inheritance===<br />
[[File:Fig13 triangulation.jpg|thumb|450px|Figure 15A. PTHR43114 before annotation]]<br />
<br />
* In the example shown in Fig 15A, 5 proteins are annotated by EXP to the GO term <code>adenine deaminase activity</code> (green squares in the 1st column of the Annotation Matrix, indicated by the red downward arrow). <br />
<br />
'''Tip:''' To view the last common ancestor that can be annotated based on triangulation(*), right click on a GO term, or anywhere in the column that contains that GO term. An inferred node, as well as its descendants, will be highlighted in grey (blue arrow, Fig 15A). <br />
* (*) '''Triangulation''' is the calculation of the last common ancestor of two sequences; in this case PAINT calculates the last common ancestor supporting an annotation to the same GO term. <br />
* Note that the node calculated by triangulation may not be the best on to annotate: the curator can decide to annotate to an more ancient or a more recent ancestor, dependent on other evidence. For example, annotations in other GO aspects may support an earlier annotation than suggested by the triangulation.<br />
* The curator should not assume that the genes in the tree are fully curated with repsect to the primary literature. It may be useful to review other papers, including reviews, to ensure annotations found in the tree accurately represents the current state of knowledge. <br />
<br />
====To annotate an ancestral node====<br />
[[File:Fig15B.jpg|thumb|450px|Figure 15B. PTHR43114 after annotation]]<br />
# Click a GO term (green square) from the Annotation Matrix (Fig. 15B) (or anywhere in the column containing the GO term).<br />
# Drag the term to the ancestral node you wish to annotate. This can be the inferred node or any other nodes. When you mouse over it, a <code>+ sign</code> will be visible next to the node. Release the mouse button to annotate. Click here for a video demo of the procedure: http://youtu.be/8kHrdiuNfos.<br />
# The node is now annotated with that term using the evidence code “IBD” (“Inferred from Biological Descendant”) (Fig. 15B).<br />
# PAINT then automatically propagates the IBD annotation to all descendants of the PAINTEed node, such that all descendants of the node will now be annotated with that term using the evidence code “IBA” (“Inferred from Biological Ancestor”). (Proteins and nodes already annotated with the term or one of its descendant terms will remain unchanged.)<br />
<br />
====Annotating an ancestral node with a qualifier====<br />
[[File:Propagating qualifiers.jpg|thumb|800px|Figure 16. Propagating qualifiers]]<br />
* If you propagate an experimental annotation that has a qualifier, ie. "NOT", "contributes_to" (for MF annotations), or "colocalizes_with" (for CC annotations), the qualifier will also get propagated, unless there are contradictory annotations, ie, annotations ''with'' and annotations ''without'' the qualifier (for the same or for different genes). In that case, a pop-up window will appear to specify whether the annotations with or without the qualifier(s) should be propagated. Click the appropriate radio button, and click on the <code>Continue</code> box to apply the selection (Fig 16).<br />
<br />
=====Notes=====<br />
* You may only annotate a node with a given GO term if '''at least one descendant''' has an annotation to that term or a child term. If you try to propagate a term with no supporting annotation, the node will turn red, and the propagation cannot be made.<br />
* Effectively, the PAINT curator only makes IBD annotations; IBA annotations are generated automatically to all descendants of the node to which an IBD annotation is made.<br />
* The IBD annotation automatically includes evidence for each of the sequences having an EXP annotation to the term or one if its descendants; it is not necessary to propagate individual EXP to generate the evidence for the annotation.<br />
<br />
===Negation of annotations: "NOT" statements===<br />
Background: Since PAINT is a model of the family's evolution, adding a NOT modifier to a descendant (either another node or a leaf) represents a loss of function during evolution, that is, we are stating that the specified function was present in an ancestral protein and has been ''lost'' in the indicated protein or clade. This is a special case of the GO guidelines for NOT, which state that a NOT annotation may be made in situations where a particular function may be expected but is absent.<br />
<br />
PAINT defines two reasons for an evolutionary loss of function, described with two separate evidence codes (ECO): <br />
* IRD = '''I'''nferred from '''R'''apid '''D'''ivergence from ancestral sequence evidence used in manual assertion: Used when there is a long branch, often following a duplication, and significant sequence divergence. For very divergent sequences, predictions are less reliable, even in the presence of a common ancestor. <br />
* IKR = '''I'''nferred from phylogenetic determination of loss of '''K'''ey '''R'''esidues evidence: Used when a residue known to be required for the activity of the protein has mutated. <br />
<br />
In both cases, the node (intermediate or leaf) on which the NOT annotation is placed gets the evidence code selected (IKR or IRD), and descendants, if any, are annotated with the IBA evidence. <br />
<br />
====To add the NOT qualifier to IBD annotations====<br />
[[File:Fig15A.jpg|thumb|450px|Figure 17A. Tree annotated with an IBD]]<br />
[[File:Fig15B.jpg|thumb|450px|Figure 17B. Pop up window to select NOT evidence]]<br />
# From a tree annotated with a IBD annotation (Fig 17A), select a node or protein to be negated. This may be either a directly annotated node or one of its children.<br />
# Click the checkbox in the NOT column of the Annotations window. <br />
# A popup menu will appear (Fig 17B). In the menu <code>Select evidence code for NOT annotation</code>, select one of the radio buttons: <br />
#* NOT due to rapid divergence<br />
#* NOT due to change in key residue(s)<br />
# '''Optional:''' In the box labeled <code>Please enter PMID and select sequence(s) from descendants providing evidence</code>, you may enter data not captured by primary annotation that support the negation. For example if a paper shows that one of the descendants does not have an activity, you can enter the PMID and select which gene was <br />
# '''Optional:''' If appropriate, you may select from the list under <code>Annotate to an ancestor term?</code>, a more general GO term to propagate to the node or sequence instead of the term negated.<br />
* In addition to the annotation no longer propagating downward, a small hash mark will appear near the node in the tree to indicate that the block exists (visible in Fig 15C). Note that a hash mark only indicates the existence of at least one NOT annotation, not that every annotation through that node is negated.<br />
<br />
'''Annotations propagated:'''<br />
[[File:Fig15C.jpg|thumb|450px|Figure 17C. Intermediate node annotated with NOT by IRK. Descendants are annotated with a NOT qualifier and IBA evidence]]<br />
[[File:Fig15D.jpg|thumb|450px|Figure 17D. Leaf node annotated with NOT by IRK.]]<br />
* If the NOT is on a node with descendants, the node will get the evidence code select (IKR or IBD), and the descendants will get an IBA evidence (Fig 17C). <br />
* If the NOT is on a leaf node it will get the evidence code select (IKR or IBD) (Fig 17D).<br />
* Upon export of PAINT annotations:<br />
** Annotations with IKR and all NOT annotations to proteins descended from that node will have the NOT qualifier added (as these have good evidence for loss of function).<br />
** Annotations with IRD and all NOT annotations to proteins descended from that node, no annotation will be exported. Thus this acts like a STOP PROPAGATION.<br />
<br />
==Removing IBD, IKR and IRD annotations==<br />
# Click on the desired node. Nodes with inferred annotations are colored orange.<br />
# Go to the Annotation tab and click the <code>Delete</code> in the Delete column (shown in a red square in Fig 13B).<br />
<br />
'''Notes:'''<br />
* Annotations and qualifiers can only be removed from the specific node to which they were made.<br />
* Primary annotations may be be changed; they may be disputed in the [https://github.com/geneontology/go-annotation/issues GO GitHub go-annotation repo].<br />
<br />
== Partial annotation of trees ==<br />
<br />
<br />
[[File:PTHR24073-RabFamily.jpg|thumb|500px|Figure 18. The RAB GTPase superfamily]]]<br />
<br />
<br />
When you want to annotate a very large family, e.g. the RAB GTPase superfamily (PTHR24073) (Fig 18), it may not be feasible to annotate all clades at the same time. In this kind of situation, you may choose to annotate only the clades you are knowledgeable and confident of, and leave other clades unexamined. When you do this, you should fully annotate the clades you choose to annotate. For example, if you choose to do the IFT27 clade, do it fully. Please don't do piecemeal annotations in various locations that may make it hard for a subsequent annotator to understand what has been done. <br />
<br />
We also agreed at the July 2014 PAINT Jamboree that you can make propagations all the way to the root if you feel that there is an ancestral role, even if you think that some clades have lost this. For example, in the RAB GTPase superfamily, we think that it had an ancestral function as a GTPase, but it is possible that some clades, e.g. the IFT22 clade, have lost this ancestral activity. You can make these high level propagations as part of your initial annotation of the family. If there are clades where this is wrong, perhaps the IBA annotation from PAINT will generate feedback that will help us correct it.<br />
<br />
=== Recording partial annotation in the notes file ===<br />
If you only partially annotate a tree, please record in the notes file which clades you have worked on using the node number, e.g. '''Eukaryota_PTN001180007''' as well as a common name, e.g. '''IFT27''', if it is helpful.<br />
<br />
==Recording trees examined, but not annotated==<br />
<br />
When you examine a tree and feel that it should not be annotated for some reason, please record that in the Evidence Notes so that we can track the fact that the family has been examined. Please use one of these tags (in all caps) in the Notes section of the Evidence tab. You can additional information after the tag if you wish (syntax between tag and additional info not discussed or determined). Then, save your annotations as normal so that PAINT will save the notes file.<br />
<br />
* '''MISSING ANNOTATION''' - Use this if the tree looks OK, but there are insufficient experimental annotations to propagate any annotations.<br />
* '''MISSING SEQUENCE''' - Use this if you feel that a specific sequence or sequences is missing. You can list the IDs of the sequence(s) after the tag.<br />
* '''BAD TREE''' - Use this if you feel that the tree has major problems beyond one or a few missing sequences.<br />
<br />
----<br />
=Interpreting the PANTHER trees=<br />
==Speciation and duplication events, and horizontal transfer==<br />
In the tree, a speciation node is shown with a circle, and a gene duplication node with an square. Horizontal transfer events also appear in the tree, though more rarely, and these are represented with a diamond.<br />
<br />
==Branch lengths==<br />
* Branch lengths show the amount of sequence divergence that has occurred between a given node and its ancestral node, in terms of the average number of amino acid substitutions per site. Shorter branches indicate less sequence divergence and therefore greater conservation of ancestral characters. A branch might be shorter because of a slower evolutionary rate (greater negative selection), or because less "time" has gone by (actually a combination of number of generations and population dynamics), or both.<br />
* Very long branches indicate an unreliable divergence estimate, due to insufficient data. Note that sometimes there is not enough data to compare all branches that descend from a given node. In this case, we have set all descendant branches to a length of 2.0 (very long branches). Branch lengths of 2.0 are often due to a sequence fragment, and at a duplication node it may also indicate a gene that has been incorrectly broken into two different genes by a gene prediction program.<br />
* Following a gene duplication (after a square node), the relative branch lengths for descendant branches are particularly useful: the shortest branch (least diverged) is more likely to have greater functional conservation.<br />
<br />
==Multiple sequence alignment (MSA)==<br />
* Some columns in the MSA have upper-case characters (and dashes '-' for insertions/deletions). These columns were used to estimate the phylogenetic tree.<br />
* Lower-case characters and periods (‘.’ for insertions/deletions) denote positions that were ignored when estimating the phylogenetic tree. Sometimes, tree errors arise because not enough columns were used, and the phylogeny could not be reconstructed well based on the included columns. Since they were not used in the phylogeny, lower-case characters can be particularly helpful in verifying the tree topology: any conserved insertions should be parsimoniously traceable to a common ancestor.<br />
<br />
----<br />
=Reporting bugs or likely errors in the trees=<br />
<br />
==Tree issues==<br />
Most often, the errors in phylogenetic trees are due to problems with the sequence alignment, or the specific MSA columns used to estimate the phylogeny. The phylogeny inference program performs fairly robust handling of sequence fragments, but sequence fragments still cause errors. Another source of error is when the sequences evolve very slowly, generating little variation from which to estimate phylogeny. In this case, the errors can usually be fixed by including additional alignment positions to consider in the phylogeny. <br />
<br />
'''If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues'''<br />
<br />
==PAINT issues==<br />
'''Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues'''<br />
<br />
=Curation Guidelines=<br />
<br />
'''Those guidelines have been published (Gaudet, Livestone, Lewis, Thomas, 2011) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059/?tool=pubmed]'''<br />
<br />
<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2021-07-01<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_User_Guide&diff=86145PAINT User Guide2023-10-17T20:28:40Z<p>Mi: /* Step 2: Open a family to curate */</p>
<hr />
<div><br />
=PAINT Overview=<br />
= PAINT (Phylogenetic Annotation and INference Tool) =<br />
PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO [[Phylogenetic Annotation Project]] to support inference of GO function terms (molecular function, cellular component and biological process) by homology.<br />
== Principles underlying PAINT ==<br />
Annotation of a gene's function by homology is often referred to as "transitive annotation", in which an experimentally-characterized function of one gene is "transferred" to another gene because of their similarity in sequence. This pairwise transfer paradigm derives from the success of sequence searching algorithms such as BLAST and Smith-Waterman. Of course, pairwise conservation of function is really due to descent from a common ancestor (homology). In other words, two sequences of sufficient length are similar because they share a common ancestor, and the reason they have a common function is most likely that they inherited that function from their common ancestor. This process can be explicitly captured using a phylogenetic model.<br />
<br />
Rather than a pairwise paradigm, PAINT uses this more accurate phylogenetic model to infer gene function by homology. PAINT annotation is intended to capture actual inferences about the evolution of gene function within a gene family: the gain, inheritance, modification and loss of function over evolutionary time. Inference is a two-step process, and involves directly annotating a phylogenetic tree. In the first step, experimental GO annotations for extant sequences are used to make inferences about when a given function may have first evolved. In PAINT, this is referred to as "up-propagation", in which ancestral genes are annotated based on information about extant sequences. In the second step, "down-propagation", ancestral annotations are used to make inferences about unannotated extant sequences, based on the principle of inheritance from the common ancestor, and allowing for modification and even loss of function during evolution.<br />
<br />
'''For a more complete description, please see the [[PAINT annotation guidelines]] and the publication on the GO Phylogenetic Annotation process, [https://www.ncbi.nlm.nih.gov/pubmed/21873635 Gaudet et al, Briefings in Bioinformatics, 2011]. '''<br />
<br />
= PAINT software =<br />
PAINT is implemented in Java by Paul Thomas's group (USC). Development of PAINT has been funded by grant GM081084 from the U.S. National Institutes of Health, and the GO Consortium grant 5U41HG002273.<br />
<br />
Software details are available in https://github.com/pantherdb/db-PAINT. Refer to https://github.com/pantherdb/db-PAINT/blob/master/README.md for implementation details.<br />
<br />
== Availability ==<br />
PAINT is freely available for download from the Panther website: https://go.paint.usc.edu/<br />
<br />
==Requirements==<br />
Java 1.8 (aka Java 8 on a Macintosh) must be installed.<br />
<br />
==Installing and configuring PAINT==<br />
PAINT is a Java application, and can be run on a either Mac or Windows. To install PAINT, download the application from: https://go.paint.usc.edu/<br />
<br />
The detailed instruction on installing and configuring the software can be found at https://go.paint.usc.edu/doc/Installation.jsp.<br />
<br />
The entire process to install the software should take no more than 10 minutes.<br />
<br />
== Data versioning ==<br />
* Phylogenetic trees are generated for [http://pantherdb.org PANTHER version 17], released on 2022-02-23.<br />
* The GO ontology version and annotations are updated monthly. <br />
<br />
----<br />
<br />
=Using PAINT=<br />
<br />
==Launching PAINT==<br />
* On a Windows machine, run the program <code>lauchPAINT.bat</code>.<br />
* On a Mac, open a Unix terminal window, go to the directory containing the PAINT program, and execute the command: <br />
<code>sh launchPAINT.sh</code> OR <code>./launchPAINT.sh</code><br />
<br />
==Login==<br />
You are required to login before you can open a tree. The purpose is to record proper acknowledgement for all the curated annotations (of tree nodes) created by you.<br />
<br />
Go to <code>File -> Login</code>.<br />
<br />
If you just want to view the tree and annotations, you can enter <code>gouser</code> as the username. The password is filled already. This is a read-only login. You can only view the tree, but can't lock the family (see below) and curate it.<br />
<br />
If you want to curate trees, enter your username and password. If you don’t have a login and password, send an email to huaiyumi@usc.edu and request one.<br />
<br />
==Curating a gene family==<br />
The analogy is to a library. You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).<br />
<br />
===Step 1: Find and "lock" families for curation===<br />
The "lock" function is only available to a curator's account. If you login to a read-only account, e.g., with "gouser" username, you can't lock a family. You can still search a family and view it.<br />
<br />
When you lock the family, other curators won’t be able to curate them. This is to prevent people from working on the same family.<br />
[[File:PAINT_search.png|thumb|Figure 1. PAINT family search box|450px]]<br />
* Go to <code>File</code> > <code>Manage and View Books...</code><br />
**A window will pop up (Fig 1). <br />
***You can search for families by various identifiers: PTHR ID, PTN ID, Gene Symbol, Protein Identifier, Gene Identifier, or gene definition.<br />
***Retrieve a list of all families, or just the uncurated families.<br />
***Retrieve a list of families that require review (incompletely curated).<br />
**Press the "submit" button to launch search<br />
[[File:PAINT_family_search_results.png|thumb|Figure 2. PAINT family search results|450px]]<br />
* Select one or several families to lock. Fig 2 shows an example when all uncurated families are returned. There are 4 possible curation status states:<br />
**Manually curated – These are the families curated, and the curator believes that the curation is complete.<br />
**Locked – Those families are locked by a curator. The name of the curator who locks the family is shown in the Locked by column. <br />
**Partially curated – These are the families that have been curated. The curator can unlock the family and leave it as partially curated.<br />
**Require PAINT review – The previously curated paint annotations are changed due to updates in either PANTHER and GO.<br />
**Unknown – These are uncurated families.<br />
*Check the box in the <code>Lock/Unlock</code> column of the families you want to check out, and click <code>Lock or Unlock selected Books</code> button at the bottom of the panel.<br />
<br />
===Step 2: Open a family to curate===<br />
* To open a family, click <code>View Locked Books</code>, and then click the <code>View</code> button (Fig 3). If you login a read-only account, you can click the <code>View</code> button as shown in Fig 2.<br />
* A family can only be locked by a single user. If a family is already locked, you can open it in View Only mode.<br />
* You can only curate families you have locked.<br />
<br />
[[File:PAINT_family_opening.png|thumb|Figure 3. Opening a previously locked family.|450px]]<br />
<br />
===Step 3: Save your annotations===<br />
You can choose to save but keep the family locked so you can continue the curation later. You can also save and unlock the family. <br />
* Go to <code>File</code> > <code>Save to Database</code>. A window will pop up with the following options:<br />
**'''Cancel'''<br />
**'''Save and unlock:''' The family will be unlocked and marked as Partially Curated.<br />
**'''Save:''' The family will remain locked. The curator should do this as often as possible during the curation.<br />
**'''Save, unlock & set curated:''' The family will be marked as Manually Curated.<br />
<br />
----<br />
<br />
==Appearance and Basic Operation==<br />
===Windows===<br />
PAINT is organized into three main panels (Fig 4): <br />
[[File:PAINT-overview.png|thumb|Figure 4. Main PAINT window|500px]]<br />
* The '''upper left panel''' shows a '''[[PAINT_User_Guide#Phylogenetic_Tree |phylogenetic tree]]'''. <br />
<br />
* The '''upper right panel''' allows you to switch back and forth between (i) the '''[[PAINT_User_Guide#Annotation_matrix |Annotation Matrix]]'''; (ii) the '''[[PAINT_User_Guide#Protein_Information_table |Protein Information Table]]''' and (iii) a multiple sequence alignment '''([[PAINT_User_Guide#Multiple_sequence_alignment_.28MSA.29 |MSA]])''' of all sequences. <br />
<br />
* The '''bottom panel''' contains two tabs: '''[[PAINT_User_Guide#Annotations_window |Annotations]]''' and '''[[PAINT_User_Guide#Evidence_window |Evidence]]'''. <br />
<br />
All the tabbed panes may be resized or split out into windows.<br />
<br />
* Click on a tab (e.g., Protein Information, Evidence) to bring it to the front. <br />
* Click the icons in the tabs or the upper right corner to Undock/Dock, Minimize, Maximize, or close individual tabs or groups of tabs. <br />
* Tabs and panes may also be rearranged within a window by dragging. <br />
* Columns in the Protein Information Table can be resized.<br />
* Windows may be closed, arranged, or resized by dragging boundaries.<br />
<br />
===Recommended configuration for curation===<br />
* Bigger is better. Use as much of the monitor as you can afford. If you are using a laptop, you may wish to attach an external monitor.<br />
* Adjust the width of the window and the partition between the Tree and the Table until you are comfortable with them.<br />
<br />
----<br />
<br />
===Phylogenetic Tree===<br />
<br />
A phylogenetic tree contains nodes and branches (Fig 5). There are three types of nodes, root, internal and leaf. Leaf nodes correspond to the proteins in the tree. Root and internal nodes represent the inferred most common ancestor of the descendants. Branch length may be interpreted as time estimates between the nodes. <br />
<br />
[[File:Figure 2.png|thumb|Figure 5. PAINT phylogenetic tree|400px]]<br />
The root and internal nodes of the tree are shown as circles (speciation events) and squares (gene duplication events). If the tree has been previously curated, the nodes maybe colored in indicate the type of annotation (e.g., with inferred or experimental evidence). More details will be described in the "Making an inferrence" section of this guide. The nodes have unique identifiers that start with PTN (=PaNther Node), followed by 9 digits. Mouse over a node to see its identifier. If you right-click on a node, a menu will appear with the options to: <br />
* '''Collapse node:''' - the entire clade is collapsed to a single node (rectangle). All the descendants are hidden, but the GO term assignments to them are still available for annotation. Right-click the node again and select "Expand node" to re-expand it. <br />
* '''Reroot to node:''' - make the selected node and the root, and hide the rest of the tree. This is useful when the tree is too large. To bring back the entire tree again, use menu "Tree -> Reset Root to Main". <br />
* '''Export seq ids from leaves:''' the ids of all leave sequences descended from the node are exported to a text file<br />
* '''Prune:''' All nodes descended from the node are removed from the tree.<br />
<br />
The tree branches can be rescaled if they are too long for comfortable viewing or too short to distinguish individual nodes. The default branch scale is 50, which works for most trees. To rescale, select <code>Tree->Scale...</code> and enter a different number. <br />
<br />
====Navigating within the tree====<br />
* Click on a protein name in the tree to highlight the protein in the tree and the table. <br />
* Left-click on a node in the tree to highlight the entire clade descended from it.<br />
<br />
----<br />
<br />
===Annotation matrix===<br />
'''Note: The colors refer to the default colors in PAINT'''<br />
<br />
[[File:PAINT_main.png|thumb|Figure 6. Main PAINT window|500px]]<br />
<br />
The matrix has a row for each gene/gene product in the tree, and a column for each GO term that is directly annotated to at least one gene/gene product in the tree. The annotation matrix gives an overview of the annotations associated with any proteins in table format. It displays one of the three Gene Ontologies at a time. You can switch to a different ontology by clicking the radio button on the upper left part of the window (red arrow, Fig 6). Mouse-over the downward triangle to see the GO term (yellow circle). The terms in the annotation matrix are grouped, with the most specific terms on the left. A few very broad terms such as “protein binding” are not shown, even though they are listed in the Annotations pane.<br />
<br />
Proteins with experimental annotations (IDA, EXP, IMP, IGI, IPI, or IEP evidence codes) for a particular ontology are colored and shown in boldface (blue circles). You may select one ontology at a time to examine using the radio buttons (red arrow) at the top of the window. <br />
<br />
* Click on a protein in the tree and the corresponding row will be highlighted in the matrix. <br />
<br />
[[File:annotation_matrix_color.png|thumb|500px|Figure 7. PAINT Annotation matrix]]<br />
<br />
* The annotations of the corresponding proteins and GO terms in the matrix are shown in colored squares (Fig 7).<br />
** When you first open a tree, only the experimental annotations are shown. These are the annotations than can be used for annotating ancestral genes.<br />
*** Experimental annotations are represented by green color. If it is a direct annotation (i.e. the actual annotation is to that exact term in that column of the matrix), there is a black dot in the middle of the green square. If it is an indirect annotation (i.e. the actual annotation is to a child of the term in that column of the matrix), there is a white dot in the middle of the square.<br />
*** NOT annotations are indicated with by a red circle with a white X.<br />
** When you have annotated an ancestral node, inferred annotations are also shown in the matrix. This allows you to easily keep track of what you've already annotated.<br />
*** Inferred annotations are represented by blue color, with either a black (direct) or white (indirect) dot in the center, or X for NOT as above. <br />
<br />
* Mouse-over an annotation square to see the tool tip of the protein name and the term.<br />
* Click on the annotation square to highlight the row. All the annotations to the protein, as well as the evidences and confidence codes will be displayed in the Annotation panel (see below for more details).<br />
* Right-click (or Command-click in Mac) on the experimental annotation (green square) in the matrix will automatically highlight the inferred most recent common ancestor (MRCA) node for the term.<br />
<br />
----<br />
<br />
===Protein Information table===<br />
[[File:PAINT_protein_info.png|thumb|450px|Figure 8. Protein information table]]<br />
The phylogenetic tree is aligned with a protein information table showing additional information and linkouts to various databases ([[Media:PAINT_protein_info.png|Fig 8]]). You can adjust the relative sizes of each within the window by dragging the line in the partition separating them. Note that the identifier table contains a lot of information that can be observed by scrolling to the right.<br />
<br />
====Navigating withing the Protein Information table====<br />
<br />
* Click anywhere within a row in the table to highlight the protein in the tree and the table.<br />
* Click on one of the blue linkouts will open a link in your web browser.<br />
<br />
<br clear='all'/><br />
----<br />
<br />
===Multiple sequence alignment (MSA)===<br />
[[File:PAINT_msa.png|thumb|450px|Figure 9. Multiple Sequence Alignment view]]<br />
The trees were estimated from an MSA, which can be accessed by clicking the "MSA" button on the right panel. The default view shows the entire alignment ([[Media:PAINT_msa.png|Figure 9]]). The evolutionarily conserved part of the alignment is indicated with uppercase letters. The other less conserved region is in lowercase letters. If a sequence misses a position in the matchstate, it is called a delete state and is designated by a ''dash''. If a sequence needs to insert a position in the less conserved region in order to keep the match state region aligned, it is called an insert state and is designated by a ''dot''.<br />
<br />
The conserved columns are colored with dark blue, blue or light blue, which indicates the conservation of 80%, 60% or 40%, respectively, in the column.<br />
<br />
[[File:PAINT_MSA_domain.png|thumb|450px|Figure 10. View domains in the Multiple Sequence Alignment view]]<br />
<br />
The MSA panel can also display the following two types of data:<br />
<br />
*'''Pfam domains''' The Pfam domain data are overlaid to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Domain ([[Media:PAINT_MSA_domain.png|Figure 10]]). The domains are shown as colored bars. Mouse-over the domain bar to display a brief summary of the domain information. <br />
<br />
[[File:PAINT_MSA_key_residue.png|thumb|450px|Figure 11. View active sites in the Multiple Sequence Alignment view]]<br />
<br />
*'''Active sites''' Active site data were gathered from the UniProt and mapped to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Key Residue ([[Media:PAINT_MSA_key_residue.png|Figure 11]]). Any sequence with active site information will be displayed in bold face. Mouse over the amino acid to view active site information. Coloring is as follows:<br />
**Active site – black<br />
**Binding – Red<br />
**Metal – Orange<br />
**Multiple residue types – Magenta<br />
<br />
<br />
Toggle back and forth between the table view (“Protein Information”) and the MSA view (“MSA”) using the buttons above the table/MSA panel.<br />
<br />
Note: You can view the sequence of a hypothetical ancestral protein (node) by first collapsing the appropriate node.<br />
<br clear='all'/><br />
----<br />
<br />
===Annotations and Evidence windows===<br />
[[File:PAINT_annotation_panel.png|thumb|700px|Figure 12. The annotations window]]<br />
[[File:PAINT_evidence.jpg|thumb|400px|Figure 13. Evidence window]]<br />
To view the annotations associated with a specific protein, click on that protein in the tree or table. Annotations appear in the <code>Annotation pane</code> ([[Media:PAINT_annotation_panel.png|Fig 12]]), containing the following information:<br />
* '''ECO (Evidence code):''' The type evidence code supporting the annotation. <br />
* '''Term name:''' The GO term name and accession. Clicking on the term links out to [http://amigo.geneontology.org/amigo AmiGO]. A term with a NOT annotation is displayed as strikethrough text. <br />
* '''Reference:''' The reference supporting the annotation. Clicking on the reference links out to PubMed. IBA annotations display an internal reference, PAINT_REF:00nnnnn, where nnnnn is the numerical part of the Panther family ID. <br />
* '''With:''' This column contains the evidence to support the inference. <br />
* '''Qualifiers:''' The qualifiers 'NOT', 'colocalizes_with' and 'contributes_to' each have a column in the annotation table, and a checkbox that is checked when the qualifier is present.<br />
* '''Delete:''' This is used to remove an inference made by PAINT (see [[PAINT_User_Guide#Removing_an_IBD_annotation|Removing an IBD annotation section]] below).<br />
<br />
===Evidence window===<br />
<br />
The evidence window ([[Media:PAINT_evidence.jpg|Fig 13]]) displayed automatically generated logs of the tree curation, such as annotations, validation and changes made by the PAINT pipeline upon data release.<br />
<br />
----<br />
<br />
===Curator notes===<br />
<br />
The <code>Curator notes</code> is a text editor used to record notes on the curation process. <code>Curator notes</code> can be modified by going to the <code>File</code> > <code>Update comment</code> menu.<br />
'''NOTE: The purpose of the annotation notes is to convey important points about the annotations and the phylogenetic tree both to other annotators and to users''', so annotators should try to make the notes as clear as possible. <br />
<br />
The annotator may use the Curator notes to describe important points in the annotation process, including: <br />
* References used to annotate the family (for example, a few major reviews)<br />
* Any important points about the family topology, including potential inconsistencies in the tree<br />
* Reasons for annotating to a different node than the MRCA (most common recent ancestor), ie the node that triangulation of annotation identifies. <br />
* Link to GitHub tickets leading to review of the tree annotation.<br />
<br />
----<br />
==PAINT navigation functionality==<br />
<br />
===“Find” function===<br />
[[File:PAINT_Find.jpg|thumb|400px|Figure 14. PAINT 'Find' functionality]]<br />
The Find function (<code>Edit</code> > <code>Find…</code>, Fig 14A) allows you to search for either a gene or a GO term. Select a gene or term search using the radio buttons (Fig 14B). Searches are case-insensitive.<br />
<br />
A gene search matches against exact match of any text stored in the database, such as any sequence identifiers, gene symbol, or even gene name (red arrow, Fig 14C). The search does not return partial match (blue arrow, (Fig 14C). To do a partial match, wildcard character(s) (*) can be added before and/or after the search term. Scroll through the list of matches and click on a specific match to highlight it in the tree, table, and annotation matrix, and to display its annotations in the Annotations window.<br />
<br />
You may search GO terms using text, or you may use numbers to search for GO IDs.<br />
<br clear='all'/><br />
----<br />
<br />
==Making an inference: Transferring annotations==<br />
Ancestral nodes in the tree can be annotated with any GO term that has been experimentally annotated to one (or more) of its descendants. These “inferred” annotations can be propagated to its other descendants.<br />
===Annotating an ancestral node, and propagating to descendants by inheritance===<br />
[[File:Fig13 triangulation.jpg|thumb|450px|Figure 15A. PTHR43114 before annotation]]<br />
<br />
* In the example shown in Fig 15A, 5 proteins are annotated by EXP to the GO term <code>adenine deaminase activity</code> (green squares in the 1st column of the Annotation Matrix, indicated by the red downward arrow). <br />
<br />
'''Tip:''' To view the last common ancestor that can be annotated based on triangulation(*), right click on a GO term, or anywhere in the column that contains that GO term. An inferred node, as well as its descendants, will be highlighted in grey (blue arrow, Fig 15A). <br />
* (*) '''Triangulation''' is the calculation of the last common ancestor of two sequences; in this case PAINT calculates the last common ancestor supporting an annotation to the same GO term. <br />
* Note that the node calculated by triangulation may not be the best on to annotate: the curator can decide to annotate to an more ancient or a more recent ancestor, dependent on other evidence. For example, annotations in other GO aspects may support an earlier annotation than suggested by the triangulation.<br />
* The curator should not assume that the genes in the tree are fully curated with repsect to the primary literature. It may be useful to review other papers, including reviews, to ensure annotations found in the tree accurately represents the current state of knowledge. <br />
<br />
====To annotate an ancestral node====<br />
[[File:Fig15B.jpg|thumb|450px|Figure 15B. PTHR43114 after annotation]]<br />
# Click a GO term (green square) from the Annotation Matrix (Fig. 15B) (or anywhere in the column containing the GO term).<br />
# Drag the term to the ancestral node you wish to annotate. This can be the inferred node or any other nodes. When you mouse over it, a <code>+ sign</code> will be visible next to the node. Release the mouse button to annotate. Click here for a video demo of the procedure: http://youtu.be/8kHrdiuNfos.<br />
# The node is now annotated with that term using the evidence code “IBD” (“Inferred from Biological Descendant”) (Fig. 15B).<br />
# PAINT then automatically propagates the IBD annotation to all descendants of the PAINTEed node, such that all descendants of the node will now be annotated with that term using the evidence code “IBA” (“Inferred from Biological Ancestor”). (Proteins and nodes already annotated with the term or one of its descendant terms will remain unchanged.)<br />
<br />
====Annotating an ancestral node with a qualifier====<br />
[[File:Propagating qualifiers.jpg|thumb|800px|Figure 16. Propagating qualifiers]]<br />
* If you propagate an experimental annotation that has a qualifier, ie. "NOT", "contributes_to" (for MF annotations), or "colocalizes_with" (for CC annotations), the qualifier will also get propagated, unless there are contradictory annotations, ie, annotations ''with'' and annotations ''without'' the qualifier (for the same or for different genes). In that case, a pop-up window will appear to specify whether the annotations with or without the qualifier(s) should be propagated. Click the appropriate radio button, and click on the <code>Continue</code> box to apply the selection (Fig 16).<br />
<br />
=====Notes=====<br />
* You may only annotate a node with a given GO term if '''at least one descendant''' has an annotation to that term or a child term. If you try to propagate a term with no supporting annotation, the node will turn red, and the propagation cannot be made.<br />
* Effectively, the PAINT curator only makes IBD annotations; IBA annotations are generated automatically to all descendants of the node to which an IBD annotation is made.<br />
* The IBD annotation automatically includes evidence for each of the sequences having an EXP annotation to the term or one if its descendants; it is not necessary to propagate individual EXP to generate the evidence for the annotation.<br />
<br />
===Negation of annotations: "NOT" statements===<br />
Background: Since PAINT is a model of the family's evolution, adding a NOT modifier to a descendant (either another node or a leaf) represents a loss of function during evolution, that is, we are stating that the specified function was present in an ancestral protein and has been ''lost'' in the indicated protein or clade. This is a special case of the GO guidelines for NOT, which state that a NOT annotation may be made in situations where a particular function may be expected but is absent.<br />
<br />
PAINT defines two reasons for an evolutionary loss of function, described with two separate evidence codes (ECO): <br />
* IRD = '''I'''nferred from '''R'''apid '''D'''ivergence from ancestral sequence evidence used in manual assertion: Used when there is a long branch, often following a duplication, and significant sequence divergence. For very divergent sequences, predictions are less reliable, even in the presence of a common ancestor. <br />
* IKR = '''I'''nferred from phylogenetic determination of loss of '''K'''ey '''R'''esidues evidence: Used when a residue known to be required for the activity of the protein has mutated. <br />
<br />
In both cases, the node (intermediate or leaf) on which the NOT annotation is placed gets the evidence code selected (IKR or IRD), and descendants, if any, are annotated with the IBA evidence. <br />
<br />
====To add the NOT qualifier to IBD annotations====<br />
[[File:Fig15A.jpg|thumb|450px|Figure 17A. Tree annotated with an IBD]]<br />
[[File:Fig15B.jpg|thumb|450px|Figure 17B. Pop up window to select NOT evidence]]<br />
# From a tree annotated with a IBD annotation (Fig 17A), select a node or protein to be negated. This may be either a directly annotated node or one of its children.<br />
# Click the checkbox in the NOT column of the Annotations window. <br />
# A popup menu will appear (Fig 17B). In the menu <code>Select evidence code for NOT annotation</code>, select one of the radio buttons: <br />
#* NOT due to rapid divergence<br />
#* NOT due to change in key residue(s)<br />
# '''Optional:''' In the box labeled <code>Please enter PMID and select sequence(s) from descendants providing evidence</code>, you may enter data not captured by primary annotation that support the negation. For example if a paper shows that one of the descendants does not have an activity, you can enter the PMID and select which gene was <br />
# '''Optional:''' If appropriate, you may select from the list under <code>Annotate to an ancestor term?</code>, a more general GO term to propagate to the node or sequence instead of the term negated.<br />
* In addition to the annotation no longer propagating downward, a small hash mark will appear near the node in the tree to indicate that the block exists (visible in Fig 15C). Note that a hash mark only indicates the existence of at least one NOT annotation, not that every annotation through that node is negated.<br />
<br />
'''Annotations propagated:'''<br />
[[File:Fig15C.jpg|thumb|450px|Figure 17C. Intermediate node annotated with NOT by IRK. Descendants are annotated with a NOT qualifier and IBA evidence]]<br />
[[File:Fig15D.jpg|thumb|450px|Figure 17D. Leaf node annotated with NOT by IRK.]]<br />
* If the NOT is on a node with descendants, the node will get the evidence code select (IKR or IBD), and the descendants will get an IBA evidence (Fig 17C). <br />
* If the NOT is on a leaf node it will get the evidence code select (IKR or IBD) (Fig 17D).<br />
* Upon export of PAINT annotations:<br />
** Annotations with IKR and all NOT annotations to proteins descended from that node will have the NOT qualifier added (as these have good evidence for loss of function).<br />
** Annotations with IRD and all NOT annotations to proteins descended from that node, no annotation will be exported. Thus this acts like a STOP PROPAGATION.<br />
<br />
==Removing IBD, IKR and IRD annotations==<br />
# Click on the desired node. Nodes with inferred annotations are colored orange.<br />
# Go to the Annotation tab and click the <code>Delete</code> in the Delete column (shown in a red square in Fig 13B).<br />
<br />
'''Notes:'''<br />
* Annotations and qualifiers can only be removed from the specific node to which they were made.<br />
* Primary annotations may be be changed; they may be disputed in the [https://github.com/geneontology/go-annotation/issues GO GitHub go-annotation repo].<br />
<br />
== Partial annotation of trees ==<br />
<br />
<br />
[[File:PTHR24073-RabFamily.jpg|thumb|500px|Figure 18. The RAB GTPase superfamily]]]<br />
<br />
<br />
When you want to annotate a very large family, e.g. the RAB GTPase superfamily (PTHR24073) (Fig 18), it may not be feasible to annotate all clades at the same time. In this kind of situation, you may choose to annotate only the clades you are knowledgeable and confident of, and leave other clades unexamined. When you do this, you should fully annotate the clades you choose to annotate. For example, if you choose to do the IFT27 clade, do it fully. Please don't do piecemeal annotations in various locations that may make it hard for a subsequent annotator to understand what has been done. <br />
<br />
We also agreed at the July 2014 PAINT Jamboree that you can make propagations all the way to the root if you feel that there is an ancestral role, even if you think that some clades have lost this. For example, in the RAB GTPase superfamily, we think that it had an ancestral function as a GTPase, but it is possible that some clades, e.g. the IFT22 clade, have lost this ancestral activity. You can make these high level propagations as part of your initial annotation of the family. If there are clades where this is wrong, perhaps the IBA annotation from PAINT will generate feedback that will help us correct it.<br />
<br />
=== Recording partial annotation in the notes file ===<br />
If you only partially annotate a tree, please record in the notes file which clades you have worked on using the node number, e.g. '''Eukaryota_PTN001180007''' as well as a common name, e.g. '''IFT27''', if it is helpful.<br />
<br />
==Recording trees examined, but not annotated==<br />
<br />
When you examine a tree and feel that it should not be annotated for some reason, please record that in the Evidence Notes so that we can track the fact that the family has been examined. Please use one of these tags (in all caps) in the Notes section of the Evidence tab. You can additional information after the tag if you wish (syntax between tag and additional info not discussed or determined). Then, save your annotations as normal so that PAINT will save the notes file.<br />
<br />
* '''MISSING ANNOTATION''' - Use this if the tree looks OK, but there are insufficient experimental annotations to propagate any annotations.<br />
* '''MISSING SEQUENCE''' - Use this if you feel that a specific sequence or sequences is missing. You can list the IDs of the sequence(s) after the tag.<br />
* '''BAD TREE''' - Use this if you feel that the tree has major problems beyond one or a few missing sequences.<br />
<br />
----<br />
=Interpreting the PANTHER trees=<br />
==Speciation and duplication events, and horizontal transfer==<br />
In the tree, a speciation node is shown with a circle, and a gene duplication node with an square. Horizontal transfer events also appear in the tree, though more rarely, and these are represented with a diamond.<br />
<br />
==Branch lengths==<br />
* Branch lengths show the amount of sequence divergence that has occurred between a given node and its ancestral node, in terms of the average number of amino acid substitutions per site. Shorter branches indicate less sequence divergence and therefore greater conservation of ancestral characters. A branch might be shorter because of a slower evolutionary rate (greater negative selection), or because less "time" has gone by (actually a combination of number of generations and population dynamics), or both.<br />
* Very long branches indicate an unreliable divergence estimate, due to insufficient data. Note that sometimes there is not enough data to compare all branches that descend from a given node. In this case, we have set all descendant branches to a length of 2.0 (very long branches). Branch lengths of 2.0 are often due to a sequence fragment, and at a duplication node it may also indicate a gene that has been incorrectly broken into two different genes by a gene prediction program.<br />
* Following a gene duplication (after a square node), the relative branch lengths for descendant branches are particularly useful: the shortest branch (least diverged) is more likely to have greater functional conservation.<br />
<br />
==Multiple sequence alignment (MSA)==<br />
* Some columns in the MSA have upper-case characters (and dashes '-' for insertions/deletions). These columns were used to estimate the phylogenetic tree.<br />
* Lower-case characters and periods (‘.’ for insertions/deletions) denote positions that were ignored when estimating the phylogenetic tree. Sometimes, tree errors arise because not enough columns were used, and the phylogeny could not be reconstructed well based on the included columns. Since they were not used in the phylogeny, lower-case characters can be particularly helpful in verifying the tree topology: any conserved insertions should be parsimoniously traceable to a common ancestor.<br />
<br />
----<br />
=Reporting bugs or likely errors in the trees=<br />
<br />
==Tree issues==<br />
Most often, the errors in phylogenetic trees are due to problems with the sequence alignment, or the specific MSA columns used to estimate the phylogeny. The phylogeny inference program performs fairly robust handling of sequence fragments, but sequence fragments still cause errors. Another source of error is when the sequences evolve very slowly, generating little variation from which to estimate phylogeny. In this case, the errors can usually be fixed by including additional alignment positions to consider in the phylogeny. <br />
<br />
'''If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues'''<br />
<br />
==PAINT issues==<br />
'''Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues'''<br />
<br />
=Curation Guidelines=<br />
<br />
'''Those guidelines have been published (Gaudet, Livestone, Lewis, Thomas, 2011) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059/?tool=pubmed]'''<br />
<br />
<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2021-07-01<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_User_Guide&diff=86144PAINT User Guide2023-10-17T20:27:00Z<p>Mi: /* Step 1: Find and "lock" families for curation */</p>
<hr />
<div><br />
=PAINT Overview=<br />
= PAINT (Phylogenetic Annotation and INference Tool) =<br />
PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO [[Phylogenetic Annotation Project]] to support inference of GO function terms (molecular function, cellular component and biological process) by homology.<br />
== Principles underlying PAINT ==<br />
Annotation of a gene's function by homology is often referred to as "transitive annotation", in which an experimentally-characterized function of one gene is "transferred" to another gene because of their similarity in sequence. This pairwise transfer paradigm derives from the success of sequence searching algorithms such as BLAST and Smith-Waterman. Of course, pairwise conservation of function is really due to descent from a common ancestor (homology). In other words, two sequences of sufficient length are similar because they share a common ancestor, and the reason they have a common function is most likely that they inherited that function from their common ancestor. This process can be explicitly captured using a phylogenetic model.<br />
<br />
Rather than a pairwise paradigm, PAINT uses this more accurate phylogenetic model to infer gene function by homology. PAINT annotation is intended to capture actual inferences about the evolution of gene function within a gene family: the gain, inheritance, modification and loss of function over evolutionary time. Inference is a two-step process, and involves directly annotating a phylogenetic tree. In the first step, experimental GO annotations for extant sequences are used to make inferences about when a given function may have first evolved. In PAINT, this is referred to as "up-propagation", in which ancestral genes are annotated based on information about extant sequences. In the second step, "down-propagation", ancestral annotations are used to make inferences about unannotated extant sequences, based on the principle of inheritance from the common ancestor, and allowing for modification and even loss of function during evolution.<br />
<br />
'''For a more complete description, please see the [[PAINT annotation guidelines]] and the publication on the GO Phylogenetic Annotation process, [https://www.ncbi.nlm.nih.gov/pubmed/21873635 Gaudet et al, Briefings in Bioinformatics, 2011]. '''<br />
<br />
= PAINT software =<br />
PAINT is implemented in Java by Paul Thomas's group (USC). Development of PAINT has been funded by grant GM081084 from the U.S. National Institutes of Health, and the GO Consortium grant 5U41HG002273.<br />
<br />
Software details are available in https://github.com/pantherdb/db-PAINT. Refer to https://github.com/pantherdb/db-PAINT/blob/master/README.md for implementation details.<br />
<br />
== Availability ==<br />
PAINT is freely available for download from the Panther website: https://go.paint.usc.edu/<br />
<br />
==Requirements==<br />
Java 1.8 (aka Java 8 on a Macintosh) must be installed.<br />
<br />
==Installing and configuring PAINT==<br />
PAINT is a Java application, and can be run on a either Mac or Windows. To install PAINT, download the application from: https://go.paint.usc.edu/<br />
<br />
The detailed instruction on installing and configuring the software can be found at https://go.paint.usc.edu/doc/Installation.jsp.<br />
<br />
The entire process to install the software should take no more than 10 minutes.<br />
<br />
== Data versioning ==<br />
* Phylogenetic trees are generated for [http://pantherdb.org PANTHER version 17], released on 2022-02-23.<br />
* The GO ontology version and annotations are updated monthly. <br />
<br />
----<br />
<br />
=Using PAINT=<br />
<br />
==Launching PAINT==<br />
* On a Windows machine, run the program <code>lauchPAINT.bat</code>.<br />
* On a Mac, open a Unix terminal window, go to the directory containing the PAINT program, and execute the command: <br />
<code>sh launchPAINT.sh</code> OR <code>./launchPAINT.sh</code><br />
<br />
==Login==<br />
You are required to login before you can open a tree. The purpose is to record proper acknowledgement for all the curated annotations (of tree nodes) created by you.<br />
<br />
Go to <code>File -> Login</code>.<br />
<br />
If you just want to view the tree and annotations, you can enter <code>gouser</code> as the username. The password is filled already. This is a read-only login. You can only view the tree, but can't lock the family (see below) and curate it.<br />
<br />
If you want to curate trees, enter your username and password. If you don’t have a login and password, send an email to huaiyumi@usc.edu and request one.<br />
<br />
==Curating a gene family==<br />
The analogy is to a library. You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).<br />
<br />
===Step 1: Find and "lock" families for curation===<br />
The "lock" function is only available to a curator's account. If you login to a read-only account, e.g., with "gouser" username, you can't lock a family. You can still search a family and view it.<br />
<br />
When you lock the family, other curators won’t be able to curate them. This is to prevent people from working on the same family.<br />
[[File:PAINT_search.png|thumb|Figure 1. PAINT family search box|450px]]<br />
* Go to <code>File</code> > <code>Manage and View Books...</code><br />
**A window will pop up (Fig 1). <br />
***You can search for families by various identifiers: PTHR ID, PTN ID, Gene Symbol, Protein Identifier, Gene Identifier, or gene definition.<br />
***Retrieve a list of all families, or just the uncurated families.<br />
***Retrieve a list of families that require review (incompletely curated).<br />
**Press the "submit" button to launch search<br />
[[File:PAINT_family_search_results.png|thumb|Figure 2. PAINT family search results|450px]]<br />
* Select one or several families to lock. Fig 2 shows an example when all uncurated families are returned. There are 4 possible curation status states:<br />
**Manually curated – These are the families curated, and the curator believes that the curation is complete.<br />
**Locked – Those families are locked by a curator. The name of the curator who locks the family is shown in the Locked by column. <br />
**Partially curated – These are the families that have been curated. The curator can unlock the family and leave it as partially curated.<br />
**Require PAINT review – The previously curated paint annotations are changed due to updates in either PANTHER and GO.<br />
**Unknown – These are uncurated families.<br />
*Check the box in the <code>Lock/Unlock</code> column of the families you want to check out, and click <code>Lock or Unlock selected Books</code> button at the bottom of the panel.<br />
<br />
===Step 2: Open a family to curate===<br />
* To open a family, click <code>View Locked Books</code>, and then click the <code>View</code> button (Fig 3).<br />
* A family can only be locked by a single user. If a family is already locked, you can open it in View Only mode.<br />
* You can only curate families you have locked.<br />
<br />
[[File:PAINT_family_opening.png|thumb|Figure 3. Opening a previously locked family.|450px]]<br />
<br />
===Step 3: Save your annotations===<br />
You can choose to save but keep the family locked so you can continue the curation later. You can also save and unlock the family. <br />
* Go to <code>File</code> > <code>Save to Database</code>. A window will pop up with the following options:<br />
**'''Cancel'''<br />
**'''Save and unlock:''' The family will be unlocked and marked as Partially Curated.<br />
**'''Save:''' The family will remain locked. The curator should do this as often as possible during the curation.<br />
**'''Save, unlock & set curated:''' The family will be marked as Manually Curated.<br />
<br />
----<br />
<br />
==Appearance and Basic Operation==<br />
===Windows===<br />
PAINT is organized into three main panels (Fig 4): <br />
[[File:PAINT-overview.png|thumb|Figure 4. Main PAINT window|500px]]<br />
* The '''upper left panel''' shows a '''[[PAINT_User_Guide#Phylogenetic_Tree |phylogenetic tree]]'''. <br />
<br />
* The '''upper right panel''' allows you to switch back and forth between (i) the '''[[PAINT_User_Guide#Annotation_matrix |Annotation Matrix]]'''; (ii) the '''[[PAINT_User_Guide#Protein_Information_table |Protein Information Table]]''' and (iii) a multiple sequence alignment '''([[PAINT_User_Guide#Multiple_sequence_alignment_.28MSA.29 |MSA]])''' of all sequences. <br />
<br />
* The '''bottom panel''' contains two tabs: '''[[PAINT_User_Guide#Annotations_window |Annotations]]''' and '''[[PAINT_User_Guide#Evidence_window |Evidence]]'''. <br />
<br />
All the tabbed panes may be resized or split out into windows.<br />
<br />
* Click on a tab (e.g., Protein Information, Evidence) to bring it to the front. <br />
* Click the icons in the tabs or the upper right corner to Undock/Dock, Minimize, Maximize, or close individual tabs or groups of tabs. <br />
* Tabs and panes may also be rearranged within a window by dragging. <br />
* Columns in the Protein Information Table can be resized.<br />
* Windows may be closed, arranged, or resized by dragging boundaries.<br />
<br />
===Recommended configuration for curation===<br />
* Bigger is better. Use as much of the monitor as you can afford. If you are using a laptop, you may wish to attach an external monitor.<br />
* Adjust the width of the window and the partition between the Tree and the Table until you are comfortable with them.<br />
<br />
----<br />
<br />
===Phylogenetic Tree===<br />
<br />
A phylogenetic tree contains nodes and branches (Fig 5). There are three types of nodes, root, internal and leaf. Leaf nodes correspond to the proteins in the tree. Root and internal nodes represent the inferred most common ancestor of the descendants. Branch length may be interpreted as time estimates between the nodes. <br />
<br />
[[File:Figure 2.png|thumb|Figure 5. PAINT phylogenetic tree|400px]]<br />
The root and internal nodes of the tree are shown as circles (speciation events) and squares (gene duplication events). If the tree has been previously curated, the nodes maybe colored in indicate the type of annotation (e.g., with inferred or experimental evidence). More details will be described in the "Making an inferrence" section of this guide. The nodes have unique identifiers that start with PTN (=PaNther Node), followed by 9 digits. Mouse over a node to see its identifier. If you right-click on a node, a menu will appear with the options to: <br />
* '''Collapse node:''' - the entire clade is collapsed to a single node (rectangle). All the descendants are hidden, but the GO term assignments to them are still available for annotation. Right-click the node again and select "Expand node" to re-expand it. <br />
* '''Reroot to node:''' - make the selected node and the root, and hide the rest of the tree. This is useful when the tree is too large. To bring back the entire tree again, use menu "Tree -> Reset Root to Main". <br />
* '''Export seq ids from leaves:''' the ids of all leave sequences descended from the node are exported to a text file<br />
* '''Prune:''' All nodes descended from the node are removed from the tree.<br />
<br />
The tree branches can be rescaled if they are too long for comfortable viewing or too short to distinguish individual nodes. The default branch scale is 50, which works for most trees. To rescale, select <code>Tree->Scale...</code> and enter a different number. <br />
<br />
====Navigating within the tree====<br />
* Click on a protein name in the tree to highlight the protein in the tree and the table. <br />
* Left-click on a node in the tree to highlight the entire clade descended from it.<br />
<br />
----<br />
<br />
===Annotation matrix===<br />
'''Note: The colors refer to the default colors in PAINT'''<br />
<br />
[[File:PAINT_main.png|thumb|Figure 6. Main PAINT window|500px]]<br />
<br />
The matrix has a row for each gene/gene product in the tree, and a column for each GO term that is directly annotated to at least one gene/gene product in the tree. The annotation matrix gives an overview of the annotations associated with any proteins in table format. It displays one of the three Gene Ontologies at a time. You can switch to a different ontology by clicking the radio button on the upper left part of the window (red arrow, Fig 6). Mouse-over the downward triangle to see the GO term (yellow circle). The terms in the annotation matrix are grouped, with the most specific terms on the left. A few very broad terms such as “protein binding” are not shown, even though they are listed in the Annotations pane.<br />
<br />
Proteins with experimental annotations (IDA, EXP, IMP, IGI, IPI, or IEP evidence codes) for a particular ontology are colored and shown in boldface (blue circles). You may select one ontology at a time to examine using the radio buttons (red arrow) at the top of the window. <br />
<br />
* Click on a protein in the tree and the corresponding row will be highlighted in the matrix. <br />
<br />
[[File:annotation_matrix_color.png|thumb|500px|Figure 7. PAINT Annotation matrix]]<br />
<br />
* The annotations of the corresponding proteins and GO terms in the matrix are shown in colored squares (Fig 7).<br />
** When you first open a tree, only the experimental annotations are shown. These are the annotations than can be used for annotating ancestral genes.<br />
*** Experimental annotations are represented by green color. If it is a direct annotation (i.e. the actual annotation is to that exact term in that column of the matrix), there is a black dot in the middle of the green square. If it is an indirect annotation (i.e. the actual annotation is to a child of the term in that column of the matrix), there is a white dot in the middle of the square.<br />
*** NOT annotations are indicated with by a red circle with a white X.<br />
** When you have annotated an ancestral node, inferred annotations are also shown in the matrix. This allows you to easily keep track of what you've already annotated.<br />
*** Inferred annotations are represented by blue color, with either a black (direct) or white (indirect) dot in the center, or X for NOT as above. <br />
<br />
* Mouse-over an annotation square to see the tool tip of the protein name and the term.<br />
* Click on the annotation square to highlight the row. All the annotations to the protein, as well as the evidences and confidence codes will be displayed in the Annotation panel (see below for more details).<br />
* Right-click (or Command-click in Mac) on the experimental annotation (green square) in the matrix will automatically highlight the inferred most recent common ancestor (MRCA) node for the term.<br />
<br />
----<br />
<br />
===Protein Information table===<br />
[[File:PAINT_protein_info.png|thumb|450px|Figure 8. Protein information table]]<br />
The phylogenetic tree is aligned with a protein information table showing additional information and linkouts to various databases ([[Media:PAINT_protein_info.png|Fig 8]]). You can adjust the relative sizes of each within the window by dragging the line in the partition separating them. Note that the identifier table contains a lot of information that can be observed by scrolling to the right.<br />
<br />
====Navigating withing the Protein Information table====<br />
<br />
* Click anywhere within a row in the table to highlight the protein in the tree and the table.<br />
* Click on one of the blue linkouts will open a link in your web browser.<br />
<br />
<br clear='all'/><br />
----<br />
<br />
===Multiple sequence alignment (MSA)===<br />
[[File:PAINT_msa.png|thumb|450px|Figure 9. Multiple Sequence Alignment view]]<br />
The trees were estimated from an MSA, which can be accessed by clicking the "MSA" button on the right panel. The default view shows the entire alignment ([[Media:PAINT_msa.png|Figure 9]]). The evolutionarily conserved part of the alignment is indicated with uppercase letters. The other less conserved region is in lowercase letters. If a sequence misses a position in the matchstate, it is called a delete state and is designated by a ''dash''. If a sequence needs to insert a position in the less conserved region in order to keep the match state region aligned, it is called an insert state and is designated by a ''dot''.<br />
<br />
The conserved columns are colored with dark blue, blue or light blue, which indicates the conservation of 80%, 60% or 40%, respectively, in the column.<br />
<br />
[[File:PAINT_MSA_domain.png|thumb|450px|Figure 10. View domains in the Multiple Sequence Alignment view]]<br />
<br />
The MSA panel can also display the following two types of data:<br />
<br />
*'''Pfam domains''' The Pfam domain data are overlaid to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Domain ([[Media:PAINT_MSA_domain.png|Figure 10]]). The domains are shown as colored bars. Mouse-over the domain bar to display a brief summary of the domain information. <br />
<br />
[[File:PAINT_MSA_key_residue.png|thumb|450px|Figure 11. View active sites in the Multiple Sequence Alignment view]]<br />
<br />
*'''Active sites''' Active site data were gathered from the UniProt and mapped to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Key Residue ([[Media:PAINT_MSA_key_residue.png|Figure 11]]). Any sequence with active site information will be displayed in bold face. Mouse over the amino acid to view active site information. Coloring is as follows:<br />
**Active site – black<br />
**Binding – Red<br />
**Metal – Orange<br />
**Multiple residue types – Magenta<br />
<br />
<br />
Toggle back and forth between the table view (“Protein Information”) and the MSA view (“MSA”) using the buttons above the table/MSA panel.<br />
<br />
Note: You can view the sequence of a hypothetical ancestral protein (node) by first collapsing the appropriate node.<br />
<br clear='all'/><br />
----<br />
<br />
===Annotations and Evidence windows===<br />
[[File:PAINT_annotation_panel.png|thumb|700px|Figure 12. The annotations window]]<br />
[[File:PAINT_evidence.jpg|thumb|400px|Figure 13. Evidence window]]<br />
To view the annotations associated with a specific protein, click on that protein in the tree or table. Annotations appear in the <code>Annotation pane</code> ([[Media:PAINT_annotation_panel.png|Fig 12]]), containing the following information:<br />
* '''ECO (Evidence code):''' The type evidence code supporting the annotation. <br />
* '''Term name:''' The GO term name and accession. Clicking on the term links out to [http://amigo.geneontology.org/amigo AmiGO]. A term with a NOT annotation is displayed as strikethrough text. <br />
* '''Reference:''' The reference supporting the annotation. Clicking on the reference links out to PubMed. IBA annotations display an internal reference, PAINT_REF:00nnnnn, where nnnnn is the numerical part of the Panther family ID. <br />
* '''With:''' This column contains the evidence to support the inference. <br />
* '''Qualifiers:''' The qualifiers 'NOT', 'colocalizes_with' and 'contributes_to' each have a column in the annotation table, and a checkbox that is checked when the qualifier is present.<br />
* '''Delete:''' This is used to remove an inference made by PAINT (see [[PAINT_User_Guide#Removing_an_IBD_annotation|Removing an IBD annotation section]] below).<br />
<br />
===Evidence window===<br />
<br />
The evidence window ([[Media:PAINT_evidence.jpg|Fig 13]]) displayed automatically generated logs of the tree curation, such as annotations, validation and changes made by the PAINT pipeline upon data release.<br />
<br />
----<br />
<br />
===Curator notes===<br />
<br />
The <code>Curator notes</code> is a text editor used to record notes on the curation process. <code>Curator notes</code> can be modified by going to the <code>File</code> > <code>Update comment</code> menu.<br />
'''NOTE: The purpose of the annotation notes is to convey important points about the annotations and the phylogenetic tree both to other annotators and to users''', so annotators should try to make the notes as clear as possible. <br />
<br />
The annotator may use the Curator notes to describe important points in the annotation process, including: <br />
* References used to annotate the family (for example, a few major reviews)<br />
* Any important points about the family topology, including potential inconsistencies in the tree<br />
* Reasons for annotating to a different node than the MRCA (most common recent ancestor), ie the node that triangulation of annotation identifies. <br />
* Link to GitHub tickets leading to review of the tree annotation.<br />
<br />
----<br />
==PAINT navigation functionality==<br />
<br />
===“Find” function===<br />
[[File:PAINT_Find.jpg|thumb|400px|Figure 14. PAINT 'Find' functionality]]<br />
The Find function (<code>Edit</code> > <code>Find…</code>, Fig 14A) allows you to search for either a gene or a GO term. Select a gene or term search using the radio buttons (Fig 14B). Searches are case-insensitive.<br />
<br />
A gene search matches against exact match of any text stored in the database, such as any sequence identifiers, gene symbol, or even gene name (red arrow, Fig 14C). The search does not return partial match (blue arrow, (Fig 14C). To do a partial match, wildcard character(s) (*) can be added before and/or after the search term. Scroll through the list of matches and click on a specific match to highlight it in the tree, table, and annotation matrix, and to display its annotations in the Annotations window.<br />
<br />
You may search GO terms using text, or you may use numbers to search for GO IDs.<br />
<br clear='all'/><br />
----<br />
<br />
==Making an inference: Transferring annotations==<br />
Ancestral nodes in the tree can be annotated with any GO term that has been experimentally annotated to one (or more) of its descendants. These “inferred” annotations can be propagated to its other descendants.<br />
===Annotating an ancestral node, and propagating to descendants by inheritance===<br />
[[File:Fig13 triangulation.jpg|thumb|450px|Figure 15A. PTHR43114 before annotation]]<br />
<br />
* In the example shown in Fig 15A, 5 proteins are annotated by EXP to the GO term <code>adenine deaminase activity</code> (green squares in the 1st column of the Annotation Matrix, indicated by the red downward arrow). <br />
<br />
'''Tip:''' To view the last common ancestor that can be annotated based on triangulation(*), right click on a GO term, or anywhere in the column that contains that GO term. An inferred node, as well as its descendants, will be highlighted in grey (blue arrow, Fig 15A). <br />
* (*) '''Triangulation''' is the calculation of the last common ancestor of two sequences; in this case PAINT calculates the last common ancestor supporting an annotation to the same GO term. <br />
* Note that the node calculated by triangulation may not be the best on to annotate: the curator can decide to annotate to an more ancient or a more recent ancestor, dependent on other evidence. For example, annotations in other GO aspects may support an earlier annotation than suggested by the triangulation.<br />
* The curator should not assume that the genes in the tree are fully curated with repsect to the primary literature. It may be useful to review other papers, including reviews, to ensure annotations found in the tree accurately represents the current state of knowledge. <br />
<br />
====To annotate an ancestral node====<br />
[[File:Fig15B.jpg|thumb|450px|Figure 15B. PTHR43114 after annotation]]<br />
# Click a GO term (green square) from the Annotation Matrix (Fig. 15B) (or anywhere in the column containing the GO term).<br />
# Drag the term to the ancestral node you wish to annotate. This can be the inferred node or any other nodes. When you mouse over it, a <code>+ sign</code> will be visible next to the node. Release the mouse button to annotate. Click here for a video demo of the procedure: http://youtu.be/8kHrdiuNfos.<br />
# The node is now annotated with that term using the evidence code “IBD” (“Inferred from Biological Descendant”) (Fig. 15B).<br />
# PAINT then automatically propagates the IBD annotation to all descendants of the PAINTEed node, such that all descendants of the node will now be annotated with that term using the evidence code “IBA” (“Inferred from Biological Ancestor”). (Proteins and nodes already annotated with the term or one of its descendant terms will remain unchanged.)<br />
<br />
====Annotating an ancestral node with a qualifier====<br />
[[File:Propagating qualifiers.jpg|thumb|800px|Figure 16. Propagating qualifiers]]<br />
* If you propagate an experimental annotation that has a qualifier, ie. "NOT", "contributes_to" (for MF annotations), or "colocalizes_with" (for CC annotations), the qualifier will also get propagated, unless there are contradictory annotations, ie, annotations ''with'' and annotations ''without'' the qualifier (for the same or for different genes). In that case, a pop-up window will appear to specify whether the annotations with or without the qualifier(s) should be propagated. Click the appropriate radio button, and click on the <code>Continue</code> box to apply the selection (Fig 16).<br />
<br />
=====Notes=====<br />
* You may only annotate a node with a given GO term if '''at least one descendant''' has an annotation to that term or a child term. If you try to propagate a term with no supporting annotation, the node will turn red, and the propagation cannot be made.<br />
* Effectively, the PAINT curator only makes IBD annotations; IBA annotations are generated automatically to all descendants of the node to which an IBD annotation is made.<br />
* The IBD annotation automatically includes evidence for each of the sequences having an EXP annotation to the term or one if its descendants; it is not necessary to propagate individual EXP to generate the evidence for the annotation.<br />
<br />
===Negation of annotations: "NOT" statements===<br />
Background: Since PAINT is a model of the family's evolution, adding a NOT modifier to a descendant (either another node or a leaf) represents a loss of function during evolution, that is, we are stating that the specified function was present in an ancestral protein and has been ''lost'' in the indicated protein or clade. This is a special case of the GO guidelines for NOT, which state that a NOT annotation may be made in situations where a particular function may be expected but is absent.<br />
<br />
PAINT defines two reasons for an evolutionary loss of function, described with two separate evidence codes (ECO): <br />
* IRD = '''I'''nferred from '''R'''apid '''D'''ivergence from ancestral sequence evidence used in manual assertion: Used when there is a long branch, often following a duplication, and significant sequence divergence. For very divergent sequences, predictions are less reliable, even in the presence of a common ancestor. <br />
* IKR = '''I'''nferred from phylogenetic determination of loss of '''K'''ey '''R'''esidues evidence: Used when a residue known to be required for the activity of the protein has mutated. <br />
<br />
In both cases, the node (intermediate or leaf) on which the NOT annotation is placed gets the evidence code selected (IKR or IRD), and descendants, if any, are annotated with the IBA evidence. <br />
<br />
====To add the NOT qualifier to IBD annotations====<br />
[[File:Fig15A.jpg|thumb|450px|Figure 17A. Tree annotated with an IBD]]<br />
[[File:Fig15B.jpg|thumb|450px|Figure 17B. Pop up window to select NOT evidence]]<br />
# From a tree annotated with a IBD annotation (Fig 17A), select a node or protein to be negated. This may be either a directly annotated node or one of its children.<br />
# Click the checkbox in the NOT column of the Annotations window. <br />
# A popup menu will appear (Fig 17B). In the menu <code>Select evidence code for NOT annotation</code>, select one of the radio buttons: <br />
#* NOT due to rapid divergence<br />
#* NOT due to change in key residue(s)<br />
# '''Optional:''' In the box labeled <code>Please enter PMID and select sequence(s) from descendants providing evidence</code>, you may enter data not captured by primary annotation that support the negation. For example if a paper shows that one of the descendants does not have an activity, you can enter the PMID and select which gene was <br />
# '''Optional:''' If appropriate, you may select from the list under <code>Annotate to an ancestor term?</code>, a more general GO term to propagate to the node or sequence instead of the term negated.<br />
* In addition to the annotation no longer propagating downward, a small hash mark will appear near the node in the tree to indicate that the block exists (visible in Fig 15C). Note that a hash mark only indicates the existence of at least one NOT annotation, not that every annotation through that node is negated.<br />
<br />
'''Annotations propagated:'''<br />
[[File:Fig15C.jpg|thumb|450px|Figure 17C. Intermediate node annotated with NOT by IRK. Descendants are annotated with a NOT qualifier and IBA evidence]]<br />
[[File:Fig15D.jpg|thumb|450px|Figure 17D. Leaf node annotated with NOT by IRK.]]<br />
* If the NOT is on a node with descendants, the node will get the evidence code select (IKR or IBD), and the descendants will get an IBA evidence (Fig 17C). <br />
* If the NOT is on a leaf node it will get the evidence code select (IKR or IBD) (Fig 17D).<br />
* Upon export of PAINT annotations:<br />
** Annotations with IKR and all NOT annotations to proteins descended from that node will have the NOT qualifier added (as these have good evidence for loss of function).<br />
** Annotations with IRD and all NOT annotations to proteins descended from that node, no annotation will be exported. Thus this acts like a STOP PROPAGATION.<br />
<br />
==Removing IBD, IKR and IRD annotations==<br />
# Click on the desired node. Nodes with inferred annotations are colored orange.<br />
# Go to the Annotation tab and click the <code>Delete</code> in the Delete column (shown in a red square in Fig 13B).<br />
<br />
'''Notes:'''<br />
* Annotations and qualifiers can only be removed from the specific node to which they were made.<br />
* Primary annotations may be be changed; they may be disputed in the [https://github.com/geneontology/go-annotation/issues GO GitHub go-annotation repo].<br />
<br />
== Partial annotation of trees ==<br />
<br />
<br />
[[File:PTHR24073-RabFamily.jpg|thumb|500px|Figure 18. The RAB GTPase superfamily]]]<br />
<br />
<br />
When you want to annotate a very large family, e.g. the RAB GTPase superfamily (PTHR24073) (Fig 18), it may not be feasible to annotate all clades at the same time. In this kind of situation, you may choose to annotate only the clades you are knowledgeable and confident of, and leave other clades unexamined. When you do this, you should fully annotate the clades you choose to annotate. For example, if you choose to do the IFT27 clade, do it fully. Please don't do piecemeal annotations in various locations that may make it hard for a subsequent annotator to understand what has been done. <br />
<br />
We also agreed at the July 2014 PAINT Jamboree that you can make propagations all the way to the root if you feel that there is an ancestral role, even if you think that some clades have lost this. For example, in the RAB GTPase superfamily, we think that it had an ancestral function as a GTPase, but it is possible that some clades, e.g. the IFT22 clade, have lost this ancestral activity. You can make these high level propagations as part of your initial annotation of the family. If there are clades where this is wrong, perhaps the IBA annotation from PAINT will generate feedback that will help us correct it.<br />
<br />
=== Recording partial annotation in the notes file ===<br />
If you only partially annotate a tree, please record in the notes file which clades you have worked on using the node number, e.g. '''Eukaryota_PTN001180007''' as well as a common name, e.g. '''IFT27''', if it is helpful.<br />
<br />
==Recording trees examined, but not annotated==<br />
<br />
When you examine a tree and feel that it should not be annotated for some reason, please record that in the Evidence Notes so that we can track the fact that the family has been examined. Please use one of these tags (in all caps) in the Notes section of the Evidence tab. You can additional information after the tag if you wish (syntax between tag and additional info not discussed or determined). Then, save your annotations as normal so that PAINT will save the notes file.<br />
<br />
* '''MISSING ANNOTATION''' - Use this if the tree looks OK, but there are insufficient experimental annotations to propagate any annotations.<br />
* '''MISSING SEQUENCE''' - Use this if you feel that a specific sequence or sequences is missing. You can list the IDs of the sequence(s) after the tag.<br />
* '''BAD TREE''' - Use this if you feel that the tree has major problems beyond one or a few missing sequences.<br />
<br />
----<br />
=Interpreting the PANTHER trees=<br />
==Speciation and duplication events, and horizontal transfer==<br />
In the tree, a speciation node is shown with a circle, and a gene duplication node with an square. Horizontal transfer events also appear in the tree, though more rarely, and these are represented with a diamond.<br />
<br />
==Branch lengths==<br />
* Branch lengths show the amount of sequence divergence that has occurred between a given node and its ancestral node, in terms of the average number of amino acid substitutions per site. Shorter branches indicate less sequence divergence and therefore greater conservation of ancestral characters. A branch might be shorter because of a slower evolutionary rate (greater negative selection), or because less "time" has gone by (actually a combination of number of generations and population dynamics), or both.<br />
* Very long branches indicate an unreliable divergence estimate, due to insufficient data. Note that sometimes there is not enough data to compare all branches that descend from a given node. In this case, we have set all descendant branches to a length of 2.0 (very long branches). Branch lengths of 2.0 are often due to a sequence fragment, and at a duplication node it may also indicate a gene that has been incorrectly broken into two different genes by a gene prediction program.<br />
* Following a gene duplication (after a square node), the relative branch lengths for descendant branches are particularly useful: the shortest branch (least diverged) is more likely to have greater functional conservation.<br />
<br />
==Multiple sequence alignment (MSA)==<br />
* Some columns in the MSA have upper-case characters (and dashes '-' for insertions/deletions). These columns were used to estimate the phylogenetic tree.<br />
* Lower-case characters and periods (‘.’ for insertions/deletions) denote positions that were ignored when estimating the phylogenetic tree. Sometimes, tree errors arise because not enough columns were used, and the phylogeny could not be reconstructed well based on the included columns. Since they were not used in the phylogeny, lower-case characters can be particularly helpful in verifying the tree topology: any conserved insertions should be parsimoniously traceable to a common ancestor.<br />
<br />
----<br />
=Reporting bugs or likely errors in the trees=<br />
<br />
==Tree issues==<br />
Most often, the errors in phylogenetic trees are due to problems with the sequence alignment, or the specific MSA columns used to estimate the phylogeny. The phylogeny inference program performs fairly robust handling of sequence fragments, but sequence fragments still cause errors. Another source of error is when the sequences evolve very slowly, generating little variation from which to estimate phylogeny. In this case, the errors can usually be fixed by including additional alignment positions to consider in the phylogeny. <br />
<br />
'''If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues'''<br />
<br />
==PAINT issues==<br />
'''Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues'''<br />
<br />
=Curation Guidelines=<br />
<br />
'''Those guidelines have been published (Gaudet, Livestone, Lewis, Thomas, 2011) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059/?tool=pubmed]'''<br />
<br />
<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2021-07-01<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_User_Guide&diff=86143PAINT User Guide2023-10-17T20:23:57Z<p>Mi: /* Login */</p>
<hr />
<div><br />
=PAINT Overview=<br />
= PAINT (Phylogenetic Annotation and INference Tool) =<br />
PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO [[Phylogenetic Annotation Project]] to support inference of GO function terms (molecular function, cellular component and biological process) by homology.<br />
== Principles underlying PAINT ==<br />
Annotation of a gene's function by homology is often referred to as "transitive annotation", in which an experimentally-characterized function of one gene is "transferred" to another gene because of their similarity in sequence. This pairwise transfer paradigm derives from the success of sequence searching algorithms such as BLAST and Smith-Waterman. Of course, pairwise conservation of function is really due to descent from a common ancestor (homology). In other words, two sequences of sufficient length are similar because they share a common ancestor, and the reason they have a common function is most likely that they inherited that function from their common ancestor. This process can be explicitly captured using a phylogenetic model.<br />
<br />
Rather than a pairwise paradigm, PAINT uses this more accurate phylogenetic model to infer gene function by homology. PAINT annotation is intended to capture actual inferences about the evolution of gene function within a gene family: the gain, inheritance, modification and loss of function over evolutionary time. Inference is a two-step process, and involves directly annotating a phylogenetic tree. In the first step, experimental GO annotations for extant sequences are used to make inferences about when a given function may have first evolved. In PAINT, this is referred to as "up-propagation", in which ancestral genes are annotated based on information about extant sequences. In the second step, "down-propagation", ancestral annotations are used to make inferences about unannotated extant sequences, based on the principle of inheritance from the common ancestor, and allowing for modification and even loss of function during evolution.<br />
<br />
'''For a more complete description, please see the [[PAINT annotation guidelines]] and the publication on the GO Phylogenetic Annotation process, [https://www.ncbi.nlm.nih.gov/pubmed/21873635 Gaudet et al, Briefings in Bioinformatics, 2011]. '''<br />
<br />
= PAINT software =<br />
PAINT is implemented in Java by Paul Thomas's group (USC). Development of PAINT has been funded by grant GM081084 from the U.S. National Institutes of Health, and the GO Consortium grant 5U41HG002273.<br />
<br />
Software details are available in https://github.com/pantherdb/db-PAINT. Refer to https://github.com/pantherdb/db-PAINT/blob/master/README.md for implementation details.<br />
<br />
== Availability ==<br />
PAINT is freely available for download from the Panther website: https://go.paint.usc.edu/<br />
<br />
==Requirements==<br />
Java 1.8 (aka Java 8 on a Macintosh) must be installed.<br />
<br />
==Installing and configuring PAINT==<br />
PAINT is a Java application, and can be run on a either Mac or Windows. To install PAINT, download the application from: https://go.paint.usc.edu/<br />
<br />
The detailed instruction on installing and configuring the software can be found at https://go.paint.usc.edu/doc/Installation.jsp.<br />
<br />
The entire process to install the software should take no more than 10 minutes.<br />
<br />
== Data versioning ==<br />
* Phylogenetic trees are generated for [http://pantherdb.org PANTHER version 17], released on 2022-02-23.<br />
* The GO ontology version and annotations are updated monthly. <br />
<br />
----<br />
<br />
=Using PAINT=<br />
<br />
==Launching PAINT==<br />
* On a Windows machine, run the program <code>lauchPAINT.bat</code>.<br />
* On a Mac, open a Unix terminal window, go to the directory containing the PAINT program, and execute the command: <br />
<code>sh launchPAINT.sh</code> OR <code>./launchPAINT.sh</code><br />
<br />
==Login==<br />
You are required to login before you can open a tree. The purpose is to record proper acknowledgement for all the curated annotations (of tree nodes) created by you.<br />
<br />
Go to <code>File -> Login</code>.<br />
<br />
If you just want to view the tree and annotations, you can enter <code>gouser</code> as the username. The password is filled already. This is a read-only login. You can only view the tree, but can't lock the family (see below) and curate it.<br />
<br />
If you want to curate trees, enter your username and password. If you don’t have a login and password, send an email to huaiyumi@usc.edu and request one.<br />
<br />
==Curating a gene family==<br />
The analogy is to a library. You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).<br />
<br />
===Step 1: Find and "lock" families for curation===<br />
When you lock the family, other curators won’t be able to curate them. This is to prevent people from working on the same family.<br />
[[File:PAINT_search.png|thumb|Figure 1. PAINT family search box|450px]]<br />
* Go to <code>File</code> > <code>Manage and View Books...</code><br />
**A window will pop up (Fig 1). <br />
***You can search for families by various identifiers: PTHR ID, PTN ID, Gene Symbol, Protein Identifier, Gene Identifier, or gene definition.<br />
***Retrieve a list of all families, or just the uncurated families.<br />
***Retrieve a list of families that require review (incompletely curated).<br />
**Press the "submit" button to launch search<br />
[[File:PAINT_family_search_results.png|thumb|Figure 2. PAINT family search results|450px]]<br />
* Select one or several families to lock. Fig 2 shows an example when all uncurated families are returned. There are 4 possible curation status states:<br />
**Manually curated – These are the families curated, and the curator believes that the curation is complete.<br />
**Locked – Those families are locked by a curator. The name of the curator who locks the family is shown in the Locked by column. <br />
**Partially curated – These are the families that have been curated. The curator can unlock the family and leave it as partially curated.<br />
**Require PAINT review – The previously curated paint annotations are changed due to updates in either PANTHER and GO.<br />
**Unknown – These are uncurated families.<br />
*Check the box in the <code>Lock/Unlock</code> column of the families you want to check out, and click <code>Lock or Unlock selected Books</code> button at the bottom of the panel.<br />
<br />
===Step 2: Open a family to curate===<br />
* To open a family, click <code>View Locked Books</code>, and then click the <code>View</code> button (Fig 3).<br />
* A family can only be locked by a single user. If a family is already locked, you can open it in View Only mode.<br />
* You can only curate families you have locked.<br />
<br />
[[File:PAINT_family_opening.png|thumb|Figure 3. Opening a previously locked family.|450px]]<br />
<br />
===Step 3: Save your annotations===<br />
You can choose to save but keep the family locked so you can continue the curation later. You can also save and unlock the family. <br />
* Go to <code>File</code> > <code>Save to Database</code>. A window will pop up with the following options:<br />
**'''Cancel'''<br />
**'''Save and unlock:''' The family will be unlocked and marked as Partially Curated.<br />
**'''Save:''' The family will remain locked. The curator should do this as often as possible during the curation.<br />
**'''Save, unlock & set curated:''' The family will be marked as Manually Curated.<br />
<br />
----<br />
<br />
==Appearance and Basic Operation==<br />
===Windows===<br />
PAINT is organized into three main panels (Fig 4): <br />
[[File:PAINT-overview.png|thumb|Figure 4. Main PAINT window|500px]]<br />
* The '''upper left panel''' shows a '''[[PAINT_User_Guide#Phylogenetic_Tree |phylogenetic tree]]'''. <br />
<br />
* The '''upper right panel''' allows you to switch back and forth between (i) the '''[[PAINT_User_Guide#Annotation_matrix |Annotation Matrix]]'''; (ii) the '''[[PAINT_User_Guide#Protein_Information_table |Protein Information Table]]''' and (iii) a multiple sequence alignment '''([[PAINT_User_Guide#Multiple_sequence_alignment_.28MSA.29 |MSA]])''' of all sequences. <br />
<br />
* The '''bottom panel''' contains two tabs: '''[[PAINT_User_Guide#Annotations_window |Annotations]]''' and '''[[PAINT_User_Guide#Evidence_window |Evidence]]'''. <br />
<br />
All the tabbed panes may be resized or split out into windows.<br />
<br />
* Click on a tab (e.g., Protein Information, Evidence) to bring it to the front. <br />
* Click the icons in the tabs or the upper right corner to Undock/Dock, Minimize, Maximize, or close individual tabs or groups of tabs. <br />
* Tabs and panes may also be rearranged within a window by dragging. <br />
* Columns in the Protein Information Table can be resized.<br />
* Windows may be closed, arranged, or resized by dragging boundaries.<br />
<br />
===Recommended configuration for curation===<br />
* Bigger is better. Use as much of the monitor as you can afford. If you are using a laptop, you may wish to attach an external monitor.<br />
* Adjust the width of the window and the partition between the Tree and the Table until you are comfortable with them.<br />
<br />
----<br />
<br />
===Phylogenetic Tree===<br />
<br />
A phylogenetic tree contains nodes and branches (Fig 5). There are three types of nodes, root, internal and leaf. Leaf nodes correspond to the proteins in the tree. Root and internal nodes represent the inferred most common ancestor of the descendants. Branch length may be interpreted as time estimates between the nodes. <br />
<br />
[[File:Figure 2.png|thumb|Figure 5. PAINT phylogenetic tree|400px]]<br />
The root and internal nodes of the tree are shown as circles (speciation events) and squares (gene duplication events). If the tree has been previously curated, the nodes maybe colored in indicate the type of annotation (e.g., with inferred or experimental evidence). More details will be described in the "Making an inferrence" section of this guide. The nodes have unique identifiers that start with PTN (=PaNther Node), followed by 9 digits. Mouse over a node to see its identifier. If you right-click on a node, a menu will appear with the options to: <br />
* '''Collapse node:''' - the entire clade is collapsed to a single node (rectangle). All the descendants are hidden, but the GO term assignments to them are still available for annotation. Right-click the node again and select "Expand node" to re-expand it. <br />
* '''Reroot to node:''' - make the selected node and the root, and hide the rest of the tree. This is useful when the tree is too large. To bring back the entire tree again, use menu "Tree -> Reset Root to Main". <br />
* '''Export seq ids from leaves:''' the ids of all leave sequences descended from the node are exported to a text file<br />
* '''Prune:''' All nodes descended from the node are removed from the tree.<br />
<br />
The tree branches can be rescaled if they are too long for comfortable viewing or too short to distinguish individual nodes. The default branch scale is 50, which works for most trees. To rescale, select <code>Tree->Scale...</code> and enter a different number. <br />
<br />
====Navigating within the tree====<br />
* Click on a protein name in the tree to highlight the protein in the tree and the table. <br />
* Left-click on a node in the tree to highlight the entire clade descended from it.<br />
<br />
----<br />
<br />
===Annotation matrix===<br />
'''Note: The colors refer to the default colors in PAINT'''<br />
<br />
[[File:PAINT_main.png|thumb|Figure 6. Main PAINT window|500px]]<br />
<br />
The matrix has a row for each gene/gene product in the tree, and a column for each GO term that is directly annotated to at least one gene/gene product in the tree. The annotation matrix gives an overview of the annotations associated with any proteins in table format. It displays one of the three Gene Ontologies at a time. You can switch to a different ontology by clicking the radio button on the upper left part of the window (red arrow, Fig 6). Mouse-over the downward triangle to see the GO term (yellow circle). The terms in the annotation matrix are grouped, with the most specific terms on the left. A few very broad terms such as “protein binding” are not shown, even though they are listed in the Annotations pane.<br />
<br />
Proteins with experimental annotations (IDA, EXP, IMP, IGI, IPI, or IEP evidence codes) for a particular ontology are colored and shown in boldface (blue circles). You may select one ontology at a time to examine using the radio buttons (red arrow) at the top of the window. <br />
<br />
* Click on a protein in the tree and the corresponding row will be highlighted in the matrix. <br />
<br />
[[File:annotation_matrix_color.png|thumb|500px|Figure 7. PAINT Annotation matrix]]<br />
<br />
* The annotations of the corresponding proteins and GO terms in the matrix are shown in colored squares (Fig 7).<br />
** When you first open a tree, only the experimental annotations are shown. These are the annotations than can be used for annotating ancestral genes.<br />
*** Experimental annotations are represented by green color. If it is a direct annotation (i.e. the actual annotation is to that exact term in that column of the matrix), there is a black dot in the middle of the green square. If it is an indirect annotation (i.e. the actual annotation is to a child of the term in that column of the matrix), there is a white dot in the middle of the square.<br />
*** NOT annotations are indicated with by a red circle with a white X.<br />
** When you have annotated an ancestral node, inferred annotations are also shown in the matrix. This allows you to easily keep track of what you've already annotated.<br />
*** Inferred annotations are represented by blue color, with either a black (direct) or white (indirect) dot in the center, or X for NOT as above. <br />
<br />
* Mouse-over an annotation square to see the tool tip of the protein name and the term.<br />
* Click on the annotation square to highlight the row. All the annotations to the protein, as well as the evidences and confidence codes will be displayed in the Annotation panel (see below for more details).<br />
* Right-click (or Command-click in Mac) on the experimental annotation (green square) in the matrix will automatically highlight the inferred most recent common ancestor (MRCA) node for the term.<br />
<br />
----<br />
<br />
===Protein Information table===<br />
[[File:PAINT_protein_info.png|thumb|450px|Figure 8. Protein information table]]<br />
The phylogenetic tree is aligned with a protein information table showing additional information and linkouts to various databases ([[Media:PAINT_protein_info.png|Fig 8]]). You can adjust the relative sizes of each within the window by dragging the line in the partition separating them. Note that the identifier table contains a lot of information that can be observed by scrolling to the right.<br />
<br />
====Navigating withing the Protein Information table====<br />
<br />
* Click anywhere within a row in the table to highlight the protein in the tree and the table.<br />
* Click on one of the blue linkouts will open a link in your web browser.<br />
<br />
<br clear='all'/><br />
----<br />
<br />
===Multiple sequence alignment (MSA)===<br />
[[File:PAINT_msa.png|thumb|450px|Figure 9. Multiple Sequence Alignment view]]<br />
The trees were estimated from an MSA, which can be accessed by clicking the "MSA" button on the right panel. The default view shows the entire alignment ([[Media:PAINT_msa.png|Figure 9]]). The evolutionarily conserved part of the alignment is indicated with uppercase letters. The other less conserved region is in lowercase letters. If a sequence misses a position in the matchstate, it is called a delete state and is designated by a ''dash''. If a sequence needs to insert a position in the less conserved region in order to keep the match state region aligned, it is called an insert state and is designated by a ''dot''.<br />
<br />
The conserved columns are colored with dark blue, blue or light blue, which indicates the conservation of 80%, 60% or 40%, respectively, in the column.<br />
<br />
[[File:PAINT_MSA_domain.png|thumb|450px|Figure 10. View domains in the Multiple Sequence Alignment view]]<br />
<br />
The MSA panel can also display the following two types of data:<br />
<br />
*'''Pfam domains''' The Pfam domain data are overlaid to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Domain ([[Media:PAINT_MSA_domain.png|Figure 10]]). The domains are shown as colored bars. Mouse-over the domain bar to display a brief summary of the domain information. <br />
<br />
[[File:PAINT_MSA_key_residue.png|thumb|450px|Figure 11. View active sites in the Multiple Sequence Alignment view]]<br />
<br />
*'''Active sites''' Active site data were gathered from the UniProt and mapped to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Key Residue ([[Media:PAINT_MSA_key_residue.png|Figure 11]]). Any sequence with active site information will be displayed in bold face. Mouse over the amino acid to view active site information. Coloring is as follows:<br />
**Active site – black<br />
**Binding – Red<br />
**Metal – Orange<br />
**Multiple residue types – Magenta<br />
<br />
<br />
Toggle back and forth between the table view (“Protein Information”) and the MSA view (“MSA”) using the buttons above the table/MSA panel.<br />
<br />
Note: You can view the sequence of a hypothetical ancestral protein (node) by first collapsing the appropriate node.<br />
<br clear='all'/><br />
----<br />
<br />
===Annotations and Evidence windows===<br />
[[File:PAINT_annotation_panel.png|thumb|700px|Figure 12. The annotations window]]<br />
[[File:PAINT_evidence.jpg|thumb|400px|Figure 13. Evidence window]]<br />
To view the annotations associated with a specific protein, click on that protein in the tree or table. Annotations appear in the <code>Annotation pane</code> ([[Media:PAINT_annotation_panel.png|Fig 12]]), containing the following information:<br />
* '''ECO (Evidence code):''' The type evidence code supporting the annotation. <br />
* '''Term name:''' The GO term name and accession. Clicking on the term links out to [http://amigo.geneontology.org/amigo AmiGO]. A term with a NOT annotation is displayed as strikethrough text. <br />
* '''Reference:''' The reference supporting the annotation. Clicking on the reference links out to PubMed. IBA annotations display an internal reference, PAINT_REF:00nnnnn, where nnnnn is the numerical part of the Panther family ID. <br />
* '''With:''' This column contains the evidence to support the inference. <br />
* '''Qualifiers:''' The qualifiers 'NOT', 'colocalizes_with' and 'contributes_to' each have a column in the annotation table, and a checkbox that is checked when the qualifier is present.<br />
* '''Delete:''' This is used to remove an inference made by PAINT (see [[PAINT_User_Guide#Removing_an_IBD_annotation|Removing an IBD annotation section]] below).<br />
<br />
===Evidence window===<br />
<br />
The evidence window ([[Media:PAINT_evidence.jpg|Fig 13]]) displayed automatically generated logs of the tree curation, such as annotations, validation and changes made by the PAINT pipeline upon data release.<br />
<br />
----<br />
<br />
===Curator notes===<br />
<br />
The <code>Curator notes</code> is a text editor used to record notes on the curation process. <code>Curator notes</code> can be modified by going to the <code>File</code> > <code>Update comment</code> menu.<br />
'''NOTE: The purpose of the annotation notes is to convey important points about the annotations and the phylogenetic tree both to other annotators and to users''', so annotators should try to make the notes as clear as possible. <br />
<br />
The annotator may use the Curator notes to describe important points in the annotation process, including: <br />
* References used to annotate the family (for example, a few major reviews)<br />
* Any important points about the family topology, including potential inconsistencies in the tree<br />
* Reasons for annotating to a different node than the MRCA (most common recent ancestor), ie the node that triangulation of annotation identifies. <br />
* Link to GitHub tickets leading to review of the tree annotation.<br />
<br />
----<br />
==PAINT navigation functionality==<br />
<br />
===“Find” function===<br />
[[File:PAINT_Find.jpg|thumb|400px|Figure 14. PAINT 'Find' functionality]]<br />
The Find function (<code>Edit</code> > <code>Find…</code>, Fig 14A) allows you to search for either a gene or a GO term. Select a gene or term search using the radio buttons (Fig 14B). Searches are case-insensitive.<br />
<br />
A gene search matches against exact match of any text stored in the database, such as any sequence identifiers, gene symbol, or even gene name (red arrow, Fig 14C). The search does not return partial match (blue arrow, (Fig 14C). To do a partial match, wildcard character(s) (*) can be added before and/or after the search term. Scroll through the list of matches and click on a specific match to highlight it in the tree, table, and annotation matrix, and to display its annotations in the Annotations window.<br />
<br />
You may search GO terms using text, or you may use numbers to search for GO IDs.<br />
<br clear='all'/><br />
----<br />
<br />
==Making an inference: Transferring annotations==<br />
Ancestral nodes in the tree can be annotated with any GO term that has been experimentally annotated to one (or more) of its descendants. These “inferred” annotations can be propagated to its other descendants.<br />
===Annotating an ancestral node, and propagating to descendants by inheritance===<br />
[[File:Fig13 triangulation.jpg|thumb|450px|Figure 15A. PTHR43114 before annotation]]<br />
<br />
* In the example shown in Fig 15A, 5 proteins are annotated by EXP to the GO term <code>adenine deaminase activity</code> (green squares in the 1st column of the Annotation Matrix, indicated by the red downward arrow). <br />
<br />
'''Tip:''' To view the last common ancestor that can be annotated based on triangulation(*), right click on a GO term, or anywhere in the column that contains that GO term. An inferred node, as well as its descendants, will be highlighted in grey (blue arrow, Fig 15A). <br />
* (*) '''Triangulation''' is the calculation of the last common ancestor of two sequences; in this case PAINT calculates the last common ancestor supporting an annotation to the same GO term. <br />
* Note that the node calculated by triangulation may not be the best on to annotate: the curator can decide to annotate to an more ancient or a more recent ancestor, dependent on other evidence. For example, annotations in other GO aspects may support an earlier annotation than suggested by the triangulation.<br />
* The curator should not assume that the genes in the tree are fully curated with repsect to the primary literature. It may be useful to review other papers, including reviews, to ensure annotations found in the tree accurately represents the current state of knowledge. <br />
<br />
====To annotate an ancestral node====<br />
[[File:Fig15B.jpg|thumb|450px|Figure 15B. PTHR43114 after annotation]]<br />
# Click a GO term (green square) from the Annotation Matrix (Fig. 15B) (or anywhere in the column containing the GO term).<br />
# Drag the term to the ancestral node you wish to annotate. This can be the inferred node or any other nodes. When you mouse over it, a <code>+ sign</code> will be visible next to the node. Release the mouse button to annotate. Click here for a video demo of the procedure: http://youtu.be/8kHrdiuNfos.<br />
# The node is now annotated with that term using the evidence code “IBD” (“Inferred from Biological Descendant”) (Fig. 15B).<br />
# PAINT then automatically propagates the IBD annotation to all descendants of the PAINTEed node, such that all descendants of the node will now be annotated with that term using the evidence code “IBA” (“Inferred from Biological Ancestor”). (Proteins and nodes already annotated with the term or one of its descendant terms will remain unchanged.)<br />
<br />
====Annotating an ancestral node with a qualifier====<br />
[[File:Propagating qualifiers.jpg|thumb|800px|Figure 16. Propagating qualifiers]]<br />
* If you propagate an experimental annotation that has a qualifier, ie. "NOT", "contributes_to" (for MF annotations), or "colocalizes_with" (for CC annotations), the qualifier will also get propagated, unless there are contradictory annotations, ie, annotations ''with'' and annotations ''without'' the qualifier (for the same or for different genes). In that case, a pop-up window will appear to specify whether the annotations with or without the qualifier(s) should be propagated. Click the appropriate radio button, and click on the <code>Continue</code> box to apply the selection (Fig 16).<br />
<br />
=====Notes=====<br />
* You may only annotate a node with a given GO term if '''at least one descendant''' has an annotation to that term or a child term. If you try to propagate a term with no supporting annotation, the node will turn red, and the propagation cannot be made.<br />
* Effectively, the PAINT curator only makes IBD annotations; IBA annotations are generated automatically to all descendants of the node to which an IBD annotation is made.<br />
* The IBD annotation automatically includes evidence for each of the sequences having an EXP annotation to the term or one if its descendants; it is not necessary to propagate individual EXP to generate the evidence for the annotation.<br />
<br />
===Negation of annotations: "NOT" statements===<br />
Background: Since PAINT is a model of the family's evolution, adding a NOT modifier to a descendant (either another node or a leaf) represents a loss of function during evolution, that is, we are stating that the specified function was present in an ancestral protein and has been ''lost'' in the indicated protein or clade. This is a special case of the GO guidelines for NOT, which state that a NOT annotation may be made in situations where a particular function may be expected but is absent.<br />
<br />
PAINT defines two reasons for an evolutionary loss of function, described with two separate evidence codes (ECO): <br />
* IRD = '''I'''nferred from '''R'''apid '''D'''ivergence from ancestral sequence evidence used in manual assertion: Used when there is a long branch, often following a duplication, and significant sequence divergence. For very divergent sequences, predictions are less reliable, even in the presence of a common ancestor. <br />
* IKR = '''I'''nferred from phylogenetic determination of loss of '''K'''ey '''R'''esidues evidence: Used when a residue known to be required for the activity of the protein has mutated. <br />
<br />
In both cases, the node (intermediate or leaf) on which the NOT annotation is placed gets the evidence code selected (IKR or IRD), and descendants, if any, are annotated with the IBA evidence. <br />
<br />
====To add the NOT qualifier to IBD annotations====<br />
[[File:Fig15A.jpg|thumb|450px|Figure 17A. Tree annotated with an IBD]]<br />
[[File:Fig15B.jpg|thumb|450px|Figure 17B. Pop up window to select NOT evidence]]<br />
# From a tree annotated with a IBD annotation (Fig 17A), select a node or protein to be negated. This may be either a directly annotated node or one of its children.<br />
# Click the checkbox in the NOT column of the Annotations window. <br />
# A popup menu will appear (Fig 17B). In the menu <code>Select evidence code for NOT annotation</code>, select one of the radio buttons: <br />
#* NOT due to rapid divergence<br />
#* NOT due to change in key residue(s)<br />
# '''Optional:''' In the box labeled <code>Please enter PMID and select sequence(s) from descendants providing evidence</code>, you may enter data not captured by primary annotation that support the negation. For example if a paper shows that one of the descendants does not have an activity, you can enter the PMID and select which gene was <br />
# '''Optional:''' If appropriate, you may select from the list under <code>Annotate to an ancestor term?</code>, a more general GO term to propagate to the node or sequence instead of the term negated.<br />
* In addition to the annotation no longer propagating downward, a small hash mark will appear near the node in the tree to indicate that the block exists (visible in Fig 15C). Note that a hash mark only indicates the existence of at least one NOT annotation, not that every annotation through that node is negated.<br />
<br />
'''Annotations propagated:'''<br />
[[File:Fig15C.jpg|thumb|450px|Figure 17C. Intermediate node annotated with NOT by IRK. Descendants are annotated with a NOT qualifier and IBA evidence]]<br />
[[File:Fig15D.jpg|thumb|450px|Figure 17D. Leaf node annotated with NOT by IRK.]]<br />
* If the NOT is on a node with descendants, the node will get the evidence code select (IKR or IBD), and the descendants will get an IBA evidence (Fig 17C). <br />
* If the NOT is on a leaf node it will get the evidence code select (IKR or IBD) (Fig 17D).<br />
* Upon export of PAINT annotations:<br />
** Annotations with IKR and all NOT annotations to proteins descended from that node will have the NOT qualifier added (as these have good evidence for loss of function).<br />
** Annotations with IRD and all NOT annotations to proteins descended from that node, no annotation will be exported. Thus this acts like a STOP PROPAGATION.<br />
<br />
==Removing IBD, IKR and IRD annotations==<br />
# Click on the desired node. Nodes with inferred annotations are colored orange.<br />
# Go to the Annotation tab and click the <code>Delete</code> in the Delete column (shown in a red square in Fig 13B).<br />
<br />
'''Notes:'''<br />
* Annotations and qualifiers can only be removed from the specific node to which they were made.<br />
* Primary annotations may be be changed; they may be disputed in the [https://github.com/geneontology/go-annotation/issues GO GitHub go-annotation repo].<br />
<br />
== Partial annotation of trees ==<br />
<br />
<br />
[[File:PTHR24073-RabFamily.jpg|thumb|500px|Figure 18. The RAB GTPase superfamily]]]<br />
<br />
<br />
When you want to annotate a very large family, e.g. the RAB GTPase superfamily (PTHR24073) (Fig 18), it may not be feasible to annotate all clades at the same time. In this kind of situation, you may choose to annotate only the clades you are knowledgeable and confident of, and leave other clades unexamined. When you do this, you should fully annotate the clades you choose to annotate. For example, if you choose to do the IFT27 clade, do it fully. Please don't do piecemeal annotations in various locations that may make it hard for a subsequent annotator to understand what has been done. <br />
<br />
We also agreed at the July 2014 PAINT Jamboree that you can make propagations all the way to the root if you feel that there is an ancestral role, even if you think that some clades have lost this. For example, in the RAB GTPase superfamily, we think that it had an ancestral function as a GTPase, but it is possible that some clades, e.g. the IFT22 clade, have lost this ancestral activity. You can make these high level propagations as part of your initial annotation of the family. If there are clades where this is wrong, perhaps the IBA annotation from PAINT will generate feedback that will help us correct it.<br />
<br />
=== Recording partial annotation in the notes file ===<br />
If you only partially annotate a tree, please record in the notes file which clades you have worked on using the node number, e.g. '''Eukaryota_PTN001180007''' as well as a common name, e.g. '''IFT27''', if it is helpful.<br />
<br />
==Recording trees examined, but not annotated==<br />
<br />
When you examine a tree and feel that it should not be annotated for some reason, please record that in the Evidence Notes so that we can track the fact that the family has been examined. Please use one of these tags (in all caps) in the Notes section of the Evidence tab. You can additional information after the tag if you wish (syntax between tag and additional info not discussed or determined). Then, save your annotations as normal so that PAINT will save the notes file.<br />
<br />
* '''MISSING ANNOTATION''' - Use this if the tree looks OK, but there are insufficient experimental annotations to propagate any annotations.<br />
* '''MISSING SEQUENCE''' - Use this if you feel that a specific sequence or sequences is missing. You can list the IDs of the sequence(s) after the tag.<br />
* '''BAD TREE''' - Use this if you feel that the tree has major problems beyond one or a few missing sequences.<br />
<br />
----<br />
=Interpreting the PANTHER trees=<br />
==Speciation and duplication events, and horizontal transfer==<br />
In the tree, a speciation node is shown with a circle, and a gene duplication node with an square. Horizontal transfer events also appear in the tree, though more rarely, and these are represented with a diamond.<br />
<br />
==Branch lengths==<br />
* Branch lengths show the amount of sequence divergence that has occurred between a given node and its ancestral node, in terms of the average number of amino acid substitutions per site. Shorter branches indicate less sequence divergence and therefore greater conservation of ancestral characters. A branch might be shorter because of a slower evolutionary rate (greater negative selection), or because less "time" has gone by (actually a combination of number of generations and population dynamics), or both.<br />
* Very long branches indicate an unreliable divergence estimate, due to insufficient data. Note that sometimes there is not enough data to compare all branches that descend from a given node. In this case, we have set all descendant branches to a length of 2.0 (very long branches). Branch lengths of 2.0 are often due to a sequence fragment, and at a duplication node it may also indicate a gene that has been incorrectly broken into two different genes by a gene prediction program.<br />
* Following a gene duplication (after a square node), the relative branch lengths for descendant branches are particularly useful: the shortest branch (least diverged) is more likely to have greater functional conservation.<br />
<br />
==Multiple sequence alignment (MSA)==<br />
* Some columns in the MSA have upper-case characters (and dashes '-' for insertions/deletions). These columns were used to estimate the phylogenetic tree.<br />
* Lower-case characters and periods (‘.’ for insertions/deletions) denote positions that were ignored when estimating the phylogenetic tree. Sometimes, tree errors arise because not enough columns were used, and the phylogeny could not be reconstructed well based on the included columns. Since they were not used in the phylogeny, lower-case characters can be particularly helpful in verifying the tree topology: any conserved insertions should be parsimoniously traceable to a common ancestor.<br />
<br />
----<br />
=Reporting bugs or likely errors in the trees=<br />
<br />
==Tree issues==<br />
Most often, the errors in phylogenetic trees are due to problems with the sequence alignment, or the specific MSA columns used to estimate the phylogeny. The phylogeny inference program performs fairly robust handling of sequence fragments, but sequence fragments still cause errors. Another source of error is when the sequences evolve very slowly, generating little variation from which to estimate phylogeny. In this case, the errors can usually be fixed by including additional alignment positions to consider in the phylogeny. <br />
<br />
'''If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues'''<br />
<br />
==PAINT issues==<br />
'''Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues'''<br />
<br />
=Curation Guidelines=<br />
<br />
'''Those guidelines have been published (Gaudet, Livestone, Lewis, Thomas, 2011) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059/?tool=pubmed]'''<br />
<br />
<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2021-07-01<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_User_Guide&diff=86142PAINT User Guide2023-10-17T20:21:06Z<p>Mi: /* Installing and configuring PAINT */</p>
<hr />
<div><br />
=PAINT Overview=<br />
= PAINT (Phylogenetic Annotation and INference Tool) =<br />
PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO [[Phylogenetic Annotation Project]] to support inference of GO function terms (molecular function, cellular component and biological process) by homology.<br />
== Principles underlying PAINT ==<br />
Annotation of a gene's function by homology is often referred to as "transitive annotation", in which an experimentally-characterized function of one gene is "transferred" to another gene because of their similarity in sequence. This pairwise transfer paradigm derives from the success of sequence searching algorithms such as BLAST and Smith-Waterman. Of course, pairwise conservation of function is really due to descent from a common ancestor (homology). In other words, two sequences of sufficient length are similar because they share a common ancestor, and the reason they have a common function is most likely that they inherited that function from their common ancestor. This process can be explicitly captured using a phylogenetic model.<br />
<br />
Rather than a pairwise paradigm, PAINT uses this more accurate phylogenetic model to infer gene function by homology. PAINT annotation is intended to capture actual inferences about the evolution of gene function within a gene family: the gain, inheritance, modification and loss of function over evolutionary time. Inference is a two-step process, and involves directly annotating a phylogenetic tree. In the first step, experimental GO annotations for extant sequences are used to make inferences about when a given function may have first evolved. In PAINT, this is referred to as "up-propagation", in which ancestral genes are annotated based on information about extant sequences. In the second step, "down-propagation", ancestral annotations are used to make inferences about unannotated extant sequences, based on the principle of inheritance from the common ancestor, and allowing for modification and even loss of function during evolution.<br />
<br />
'''For a more complete description, please see the [[PAINT annotation guidelines]] and the publication on the GO Phylogenetic Annotation process, [https://www.ncbi.nlm.nih.gov/pubmed/21873635 Gaudet et al, Briefings in Bioinformatics, 2011]. '''<br />
<br />
= PAINT software =<br />
PAINT is implemented in Java by Paul Thomas's group (USC). Development of PAINT has been funded by grant GM081084 from the U.S. National Institutes of Health, and the GO Consortium grant 5U41HG002273.<br />
<br />
Software details are available in https://github.com/pantherdb/db-PAINT. Refer to https://github.com/pantherdb/db-PAINT/blob/master/README.md for implementation details.<br />
<br />
== Availability ==<br />
PAINT is freely available for download from the Panther website: https://go.paint.usc.edu/<br />
<br />
==Requirements==<br />
Java 1.8 (aka Java 8 on a Macintosh) must be installed.<br />
<br />
==Installing and configuring PAINT==<br />
PAINT is a Java application, and can be run on a either Mac or Windows. To install PAINT, download the application from: https://go.paint.usc.edu/<br />
<br />
The detailed instruction on installing and configuring the software can be found at https://go.paint.usc.edu/doc/Installation.jsp.<br />
<br />
The entire process to install the software should take no more than 10 minutes.<br />
<br />
== Data versioning ==<br />
* Phylogenetic trees are generated for [http://pantherdb.org PANTHER version 17], released on 2022-02-23.<br />
* The GO ontology version and annotations are updated monthly. <br />
<br />
----<br />
<br />
=Using PAINT=<br />
<br />
==Launching PAINT==<br />
* On a Windows machine, run the program <code>lauchPAINT.bat</code>.<br />
* On a Mac, open a Unix terminal window, go to the directory containing the PAINT program, and execute the command: <br />
<code>sh launchPAINT.sh</code> OR <code>./launchPAINT.sh</code><br />
<br />
==Login==<br />
You are required to login before you can open a tree. The purpose is to record proper acknowledgement for all the curated annotations (of tree nodes) created by you.<br />
<br />
Go to <code>File -> Login</code>.<br />
<br />
If you just want to view the tree and annotations, you can enter <code>gouser</code> as the username. The password is filled already. This is a read-only login.<br />
<br />
If you want to curate trees, enter your username and password. If you don’t have a login and password, send an email to huaiyumi@usc.edu and request one.<br />
<br />
==Curating a gene family==<br />
The analogy is to a library. You will first find and check out (lock) the families you want to curate, and then select a family to curate from your list of locked families. All families now have a curation status (curated, partially curated, uncurated).<br />
<br />
===Step 1: Find and "lock" families for curation===<br />
When you lock the family, other curators won’t be able to curate them. This is to prevent people from working on the same family.<br />
[[File:PAINT_search.png|thumb|Figure 1. PAINT family search box|450px]]<br />
* Go to <code>File</code> > <code>Manage and View Books...</code><br />
**A window will pop up (Fig 1). <br />
***You can search for families by various identifiers: PTHR ID, PTN ID, Gene Symbol, Protein Identifier, Gene Identifier, or gene definition.<br />
***Retrieve a list of all families, or just the uncurated families.<br />
***Retrieve a list of families that require review (incompletely curated).<br />
**Press the "submit" button to launch search<br />
[[File:PAINT_family_search_results.png|thumb|Figure 2. PAINT family search results|450px]]<br />
* Select one or several families to lock. Fig 2 shows an example when all uncurated families are returned. There are 4 possible curation status states:<br />
**Manually curated – These are the families curated, and the curator believes that the curation is complete.<br />
**Locked – Those families are locked by a curator. The name of the curator who locks the family is shown in the Locked by column. <br />
**Partially curated – These are the families that have been curated. The curator can unlock the family and leave it as partially curated.<br />
**Require PAINT review – The previously curated paint annotations are changed due to updates in either PANTHER and GO.<br />
**Unknown – These are uncurated families.<br />
*Check the box in the <code>Lock/Unlock</code> column of the families you want to check out, and click <code>Lock or Unlock selected Books</code> button at the bottom of the panel.<br />
<br />
===Step 2: Open a family to curate===<br />
* To open a family, click <code>View Locked Books</code>, and then click the <code>View</code> button (Fig 3).<br />
* A family can only be locked by a single user. If a family is already locked, you can open it in View Only mode.<br />
* You can only curate families you have locked.<br />
<br />
[[File:PAINT_family_opening.png|thumb|Figure 3. Opening a previously locked family.|450px]]<br />
<br />
===Step 3: Save your annotations===<br />
You can choose to save but keep the family locked so you can continue the curation later. You can also save and unlock the family. <br />
* Go to <code>File</code> > <code>Save to Database</code>. A window will pop up with the following options:<br />
**'''Cancel'''<br />
**'''Save and unlock:''' The family will be unlocked and marked as Partially Curated.<br />
**'''Save:''' The family will remain locked. The curator should do this as often as possible during the curation.<br />
**'''Save, unlock & set curated:''' The family will be marked as Manually Curated.<br />
<br />
----<br />
<br />
==Appearance and Basic Operation==<br />
===Windows===<br />
PAINT is organized into three main panels (Fig 4): <br />
[[File:PAINT-overview.png|thumb|Figure 4. Main PAINT window|500px]]<br />
* The '''upper left panel''' shows a '''[[PAINT_User_Guide#Phylogenetic_Tree |phylogenetic tree]]'''. <br />
<br />
* The '''upper right panel''' allows you to switch back and forth between (i) the '''[[PAINT_User_Guide#Annotation_matrix |Annotation Matrix]]'''; (ii) the '''[[PAINT_User_Guide#Protein_Information_table |Protein Information Table]]''' and (iii) a multiple sequence alignment '''([[PAINT_User_Guide#Multiple_sequence_alignment_.28MSA.29 |MSA]])''' of all sequences. <br />
<br />
* The '''bottom panel''' contains two tabs: '''[[PAINT_User_Guide#Annotations_window |Annotations]]''' and '''[[PAINT_User_Guide#Evidence_window |Evidence]]'''. <br />
<br />
All the tabbed panes may be resized or split out into windows.<br />
<br />
* Click on a tab (e.g., Protein Information, Evidence) to bring it to the front. <br />
* Click the icons in the tabs or the upper right corner to Undock/Dock, Minimize, Maximize, or close individual tabs or groups of tabs. <br />
* Tabs and panes may also be rearranged within a window by dragging. <br />
* Columns in the Protein Information Table can be resized.<br />
* Windows may be closed, arranged, or resized by dragging boundaries.<br />
<br />
===Recommended configuration for curation===<br />
* Bigger is better. Use as much of the monitor as you can afford. If you are using a laptop, you may wish to attach an external monitor.<br />
* Adjust the width of the window and the partition between the Tree and the Table until you are comfortable with them.<br />
<br />
----<br />
<br />
===Phylogenetic Tree===<br />
<br />
A phylogenetic tree contains nodes and branches (Fig 5). There are three types of nodes, root, internal and leaf. Leaf nodes correspond to the proteins in the tree. Root and internal nodes represent the inferred most common ancestor of the descendants. Branch length may be interpreted as time estimates between the nodes. <br />
<br />
[[File:Figure 2.png|thumb|Figure 5. PAINT phylogenetic tree|400px]]<br />
The root and internal nodes of the tree are shown as circles (speciation events) and squares (gene duplication events). If the tree has been previously curated, the nodes maybe colored in indicate the type of annotation (e.g., with inferred or experimental evidence). More details will be described in the "Making an inferrence" section of this guide. The nodes have unique identifiers that start with PTN (=PaNther Node), followed by 9 digits. Mouse over a node to see its identifier. If you right-click on a node, a menu will appear with the options to: <br />
* '''Collapse node:''' - the entire clade is collapsed to a single node (rectangle). All the descendants are hidden, but the GO term assignments to them are still available for annotation. Right-click the node again and select "Expand node" to re-expand it. <br />
* '''Reroot to node:''' - make the selected node and the root, and hide the rest of the tree. This is useful when the tree is too large. To bring back the entire tree again, use menu "Tree -> Reset Root to Main". <br />
* '''Export seq ids from leaves:''' the ids of all leave sequences descended from the node are exported to a text file<br />
* '''Prune:''' All nodes descended from the node are removed from the tree.<br />
<br />
The tree branches can be rescaled if they are too long for comfortable viewing or too short to distinguish individual nodes. The default branch scale is 50, which works for most trees. To rescale, select <code>Tree->Scale...</code> and enter a different number. <br />
<br />
====Navigating within the tree====<br />
* Click on a protein name in the tree to highlight the protein in the tree and the table. <br />
* Left-click on a node in the tree to highlight the entire clade descended from it.<br />
<br />
----<br />
<br />
===Annotation matrix===<br />
'''Note: The colors refer to the default colors in PAINT'''<br />
<br />
[[File:PAINT_main.png|thumb|Figure 6. Main PAINT window|500px]]<br />
<br />
The matrix has a row for each gene/gene product in the tree, and a column for each GO term that is directly annotated to at least one gene/gene product in the tree. The annotation matrix gives an overview of the annotations associated with any proteins in table format. It displays one of the three Gene Ontologies at a time. You can switch to a different ontology by clicking the radio button on the upper left part of the window (red arrow, Fig 6). Mouse-over the downward triangle to see the GO term (yellow circle). The terms in the annotation matrix are grouped, with the most specific terms on the left. A few very broad terms such as “protein binding” are not shown, even though they are listed in the Annotations pane.<br />
<br />
Proteins with experimental annotations (IDA, EXP, IMP, IGI, IPI, or IEP evidence codes) for a particular ontology are colored and shown in boldface (blue circles). You may select one ontology at a time to examine using the radio buttons (red arrow) at the top of the window. <br />
<br />
* Click on a protein in the tree and the corresponding row will be highlighted in the matrix. <br />
<br />
[[File:annotation_matrix_color.png|thumb|500px|Figure 7. PAINT Annotation matrix]]<br />
<br />
* The annotations of the corresponding proteins and GO terms in the matrix are shown in colored squares (Fig 7).<br />
** When you first open a tree, only the experimental annotations are shown. These are the annotations than can be used for annotating ancestral genes.<br />
*** Experimental annotations are represented by green color. If it is a direct annotation (i.e. the actual annotation is to that exact term in that column of the matrix), there is a black dot in the middle of the green square. If it is an indirect annotation (i.e. the actual annotation is to a child of the term in that column of the matrix), there is a white dot in the middle of the square.<br />
*** NOT annotations are indicated with by a red circle with a white X.<br />
** When you have annotated an ancestral node, inferred annotations are also shown in the matrix. This allows you to easily keep track of what you've already annotated.<br />
*** Inferred annotations are represented by blue color, with either a black (direct) or white (indirect) dot in the center, or X for NOT as above. <br />
<br />
* Mouse-over an annotation square to see the tool tip of the protein name and the term.<br />
* Click on the annotation square to highlight the row. All the annotations to the protein, as well as the evidences and confidence codes will be displayed in the Annotation panel (see below for more details).<br />
* Right-click (or Command-click in Mac) on the experimental annotation (green square) in the matrix will automatically highlight the inferred most recent common ancestor (MRCA) node for the term.<br />
<br />
----<br />
<br />
===Protein Information table===<br />
[[File:PAINT_protein_info.png|thumb|450px|Figure 8. Protein information table]]<br />
The phylogenetic tree is aligned with a protein information table showing additional information and linkouts to various databases ([[Media:PAINT_protein_info.png|Fig 8]]). You can adjust the relative sizes of each within the window by dragging the line in the partition separating them. Note that the identifier table contains a lot of information that can be observed by scrolling to the right.<br />
<br />
====Navigating withing the Protein Information table====<br />
<br />
* Click anywhere within a row in the table to highlight the protein in the tree and the table.<br />
* Click on one of the blue linkouts will open a link in your web browser.<br />
<br />
<br clear='all'/><br />
----<br />
<br />
===Multiple sequence alignment (MSA)===<br />
[[File:PAINT_msa.png|thumb|450px|Figure 9. Multiple Sequence Alignment view]]<br />
The trees were estimated from an MSA, which can be accessed by clicking the "MSA" button on the right panel. The default view shows the entire alignment ([[Media:PAINT_msa.png|Figure 9]]). The evolutionarily conserved part of the alignment is indicated with uppercase letters. The other less conserved region is in lowercase letters. If a sequence misses a position in the matchstate, it is called a delete state and is designated by a ''dash''. If a sequence needs to insert a position in the less conserved region in order to keep the match state region aligned, it is called an insert state and is designated by a ''dot''.<br />
<br />
The conserved columns are colored with dark blue, blue or light blue, which indicates the conservation of 80%, 60% or 40%, respectively, in the column.<br />
<br />
[[File:PAINT_MSA_domain.png|thumb|450px|Figure 10. View domains in the Multiple Sequence Alignment view]]<br />
<br />
The MSA panel can also display the following two types of data:<br />
<br />
*'''Pfam domains''' The Pfam domain data are overlaid to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Domain ([[Media:PAINT_MSA_domain.png|Figure 10]]). The domains are shown as colored bars. Mouse-over the domain bar to display a brief summary of the domain information. <br />
<br />
[[File:PAINT_MSA_key_residue.png|thumb|450px|Figure 11. View active sites in the Multiple Sequence Alignment view]]<br />
<br />
*'''Active sites''' Active site data were gathered from the UniProt and mapped to the MSA. They can be accessed in the MSA tab via Menu MSA and Domain->Key Residue ([[Media:PAINT_MSA_key_residue.png|Figure 11]]). Any sequence with active site information will be displayed in bold face. Mouse over the amino acid to view active site information. Coloring is as follows:<br />
**Active site – black<br />
**Binding – Red<br />
**Metal – Orange<br />
**Multiple residue types – Magenta<br />
<br />
<br />
Toggle back and forth between the table view (“Protein Information”) and the MSA view (“MSA”) using the buttons above the table/MSA panel.<br />
<br />
Note: You can view the sequence of a hypothetical ancestral protein (node) by first collapsing the appropriate node.<br />
<br clear='all'/><br />
----<br />
<br />
===Annotations and Evidence windows===<br />
[[File:PAINT_annotation_panel.png|thumb|700px|Figure 12. The annotations window]]<br />
[[File:PAINT_evidence.jpg|thumb|400px|Figure 13. Evidence window]]<br />
To view the annotations associated with a specific protein, click on that protein in the tree or table. Annotations appear in the <code>Annotation pane</code> ([[Media:PAINT_annotation_panel.png|Fig 12]]), containing the following information:<br />
* '''ECO (Evidence code):''' The type evidence code supporting the annotation. <br />
* '''Term name:''' The GO term name and accession. Clicking on the term links out to [http://amigo.geneontology.org/amigo AmiGO]. A term with a NOT annotation is displayed as strikethrough text. <br />
* '''Reference:''' The reference supporting the annotation. Clicking on the reference links out to PubMed. IBA annotations display an internal reference, PAINT_REF:00nnnnn, where nnnnn is the numerical part of the Panther family ID. <br />
* '''With:''' This column contains the evidence to support the inference. <br />
* '''Qualifiers:''' The qualifiers 'NOT', 'colocalizes_with' and 'contributes_to' each have a column in the annotation table, and a checkbox that is checked when the qualifier is present.<br />
* '''Delete:''' This is used to remove an inference made by PAINT (see [[PAINT_User_Guide#Removing_an_IBD_annotation|Removing an IBD annotation section]] below).<br />
<br />
===Evidence window===<br />
<br />
The evidence window ([[Media:PAINT_evidence.jpg|Fig 13]]) displayed automatically generated logs of the tree curation, such as annotations, validation and changes made by the PAINT pipeline upon data release.<br />
<br />
----<br />
<br />
===Curator notes===<br />
<br />
The <code>Curator notes</code> is a text editor used to record notes on the curation process. <code>Curator notes</code> can be modified by going to the <code>File</code> > <code>Update comment</code> menu.<br />
'''NOTE: The purpose of the annotation notes is to convey important points about the annotations and the phylogenetic tree both to other annotators and to users''', so annotators should try to make the notes as clear as possible. <br />
<br />
The annotator may use the Curator notes to describe important points in the annotation process, including: <br />
* References used to annotate the family (for example, a few major reviews)<br />
* Any important points about the family topology, including potential inconsistencies in the tree<br />
* Reasons for annotating to a different node than the MRCA (most common recent ancestor), ie the node that triangulation of annotation identifies. <br />
* Link to GitHub tickets leading to review of the tree annotation.<br />
<br />
----<br />
==PAINT navigation functionality==<br />
<br />
===“Find” function===<br />
[[File:PAINT_Find.jpg|thumb|400px|Figure 14. PAINT 'Find' functionality]]<br />
The Find function (<code>Edit</code> > <code>Find…</code>, Fig 14A) allows you to search for either a gene or a GO term. Select a gene or term search using the radio buttons (Fig 14B). Searches are case-insensitive.<br />
<br />
A gene search matches against exact match of any text stored in the database, such as any sequence identifiers, gene symbol, or even gene name (red arrow, Fig 14C). The search does not return partial match (blue arrow, (Fig 14C). To do a partial match, wildcard character(s) (*) can be added before and/or after the search term. Scroll through the list of matches and click on a specific match to highlight it in the tree, table, and annotation matrix, and to display its annotations in the Annotations window.<br />
<br />
You may search GO terms using text, or you may use numbers to search for GO IDs.<br />
<br clear='all'/><br />
----<br />
<br />
==Making an inference: Transferring annotations==<br />
Ancestral nodes in the tree can be annotated with any GO term that has been experimentally annotated to one (or more) of its descendants. These “inferred” annotations can be propagated to its other descendants.<br />
===Annotating an ancestral node, and propagating to descendants by inheritance===<br />
[[File:Fig13 triangulation.jpg|thumb|450px|Figure 15A. PTHR43114 before annotation]]<br />
<br />
* In the example shown in Fig 15A, 5 proteins are annotated by EXP to the GO term <code>adenine deaminase activity</code> (green squares in the 1st column of the Annotation Matrix, indicated by the red downward arrow). <br />
<br />
'''Tip:''' To view the last common ancestor that can be annotated based on triangulation(*), right click on a GO term, or anywhere in the column that contains that GO term. An inferred node, as well as its descendants, will be highlighted in grey (blue arrow, Fig 15A). <br />
* (*) '''Triangulation''' is the calculation of the last common ancestor of two sequences; in this case PAINT calculates the last common ancestor supporting an annotation to the same GO term. <br />
* Note that the node calculated by triangulation may not be the best on to annotate: the curator can decide to annotate to an more ancient or a more recent ancestor, dependent on other evidence. For example, annotations in other GO aspects may support an earlier annotation than suggested by the triangulation.<br />
* The curator should not assume that the genes in the tree are fully curated with repsect to the primary literature. It may be useful to review other papers, including reviews, to ensure annotations found in the tree accurately represents the current state of knowledge. <br />
<br />
====To annotate an ancestral node====<br />
[[File:Fig15B.jpg|thumb|450px|Figure 15B. PTHR43114 after annotation]]<br />
# Click a GO term (green square) from the Annotation Matrix (Fig. 15B) (or anywhere in the column containing the GO term).<br />
# Drag the term to the ancestral node you wish to annotate. This can be the inferred node or any other nodes. When you mouse over it, a <code>+ sign</code> will be visible next to the node. Release the mouse button to annotate. Click here for a video demo of the procedure: http://youtu.be/8kHrdiuNfos.<br />
# The node is now annotated with that term using the evidence code “IBD” (“Inferred from Biological Descendant”) (Fig. 15B).<br />
# PAINT then automatically propagates the IBD annotation to all descendants of the PAINTEed node, such that all descendants of the node will now be annotated with that term using the evidence code “IBA” (“Inferred from Biological Ancestor”). (Proteins and nodes already annotated with the term or one of its descendant terms will remain unchanged.)<br />
<br />
====Annotating an ancestral node with a qualifier====<br />
[[File:Propagating qualifiers.jpg|thumb|800px|Figure 16. Propagating qualifiers]]<br />
* If you propagate an experimental annotation that has a qualifier, ie. "NOT", "contributes_to" (for MF annotations), or "colocalizes_with" (for CC annotations), the qualifier will also get propagated, unless there are contradictory annotations, ie, annotations ''with'' and annotations ''without'' the qualifier (for the same or for different genes). In that case, a pop-up window will appear to specify whether the annotations with or without the qualifier(s) should be propagated. Click the appropriate radio button, and click on the <code>Continue</code> box to apply the selection (Fig 16).<br />
<br />
=====Notes=====<br />
* You may only annotate a node with a given GO term if '''at least one descendant''' has an annotation to that term or a child term. If you try to propagate a term with no supporting annotation, the node will turn red, and the propagation cannot be made.<br />
* Effectively, the PAINT curator only makes IBD annotations; IBA annotations are generated automatically to all descendants of the node to which an IBD annotation is made.<br />
* The IBD annotation automatically includes evidence for each of the sequences having an EXP annotation to the term or one if its descendants; it is not necessary to propagate individual EXP to generate the evidence for the annotation.<br />
<br />
===Negation of annotations: "NOT" statements===<br />
Background: Since PAINT is a model of the family's evolution, adding a NOT modifier to a descendant (either another node or a leaf) represents a loss of function during evolution, that is, we are stating that the specified function was present in an ancestral protein and has been ''lost'' in the indicated protein or clade. This is a special case of the GO guidelines for NOT, which state that a NOT annotation may be made in situations where a particular function may be expected but is absent.<br />
<br />
PAINT defines two reasons for an evolutionary loss of function, described with two separate evidence codes (ECO): <br />
* IRD = '''I'''nferred from '''R'''apid '''D'''ivergence from ancestral sequence evidence used in manual assertion: Used when there is a long branch, often following a duplication, and significant sequence divergence. For very divergent sequences, predictions are less reliable, even in the presence of a common ancestor. <br />
* IKR = '''I'''nferred from phylogenetic determination of loss of '''K'''ey '''R'''esidues evidence: Used when a residue known to be required for the activity of the protein has mutated. <br />
<br />
In both cases, the node (intermediate or leaf) on which the NOT annotation is placed gets the evidence code selected (IKR or IRD), and descendants, if any, are annotated with the IBA evidence. <br />
<br />
====To add the NOT qualifier to IBD annotations====<br />
[[File:Fig15A.jpg|thumb|450px|Figure 17A. Tree annotated with an IBD]]<br />
[[File:Fig15B.jpg|thumb|450px|Figure 17B. Pop up window to select NOT evidence]]<br />
# From a tree annotated with a IBD annotation (Fig 17A), select a node or protein to be negated. This may be either a directly annotated node or one of its children.<br />
# Click the checkbox in the NOT column of the Annotations window. <br />
# A popup menu will appear (Fig 17B). In the menu <code>Select evidence code for NOT annotation</code>, select one of the radio buttons: <br />
#* NOT due to rapid divergence<br />
#* NOT due to change in key residue(s)<br />
# '''Optional:''' In the box labeled <code>Please enter PMID and select sequence(s) from descendants providing evidence</code>, you may enter data not captured by primary annotation that support the negation. For example if a paper shows that one of the descendants does not have an activity, you can enter the PMID and select which gene was <br />
# '''Optional:''' If appropriate, you may select from the list under <code>Annotate to an ancestor term?</code>, a more general GO term to propagate to the node or sequence instead of the term negated.<br />
* In addition to the annotation no longer propagating downward, a small hash mark will appear near the node in the tree to indicate that the block exists (visible in Fig 15C). Note that a hash mark only indicates the existence of at least one NOT annotation, not that every annotation through that node is negated.<br />
<br />
'''Annotations propagated:'''<br />
[[File:Fig15C.jpg|thumb|450px|Figure 17C. Intermediate node annotated with NOT by IRK. Descendants are annotated with a NOT qualifier and IBA evidence]]<br />
[[File:Fig15D.jpg|thumb|450px|Figure 17D. Leaf node annotated with NOT by IRK.]]<br />
* If the NOT is on a node with descendants, the node will get the evidence code select (IKR or IBD), and the descendants will get an IBA evidence (Fig 17C). <br />
* If the NOT is on a leaf node it will get the evidence code select (IKR or IBD) (Fig 17D).<br />
* Upon export of PAINT annotations:<br />
** Annotations with IKR and all NOT annotations to proteins descended from that node will have the NOT qualifier added (as these have good evidence for loss of function).<br />
** Annotations with IRD and all NOT annotations to proteins descended from that node, no annotation will be exported. Thus this acts like a STOP PROPAGATION.<br />
<br />
==Removing IBD, IKR and IRD annotations==<br />
# Click on the desired node. Nodes with inferred annotations are colored orange.<br />
# Go to the Annotation tab and click the <code>Delete</code> in the Delete column (shown in a red square in Fig 13B).<br />
<br />
'''Notes:'''<br />
* Annotations and qualifiers can only be removed from the specific node to which they were made.<br />
* Primary annotations may be be changed; they may be disputed in the [https://github.com/geneontology/go-annotation/issues GO GitHub go-annotation repo].<br />
<br />
== Partial annotation of trees ==<br />
<br />
<br />
[[File:PTHR24073-RabFamily.jpg|thumb|500px|Figure 18. The RAB GTPase superfamily]]]<br />
<br />
<br />
When you want to annotate a very large family, e.g. the RAB GTPase superfamily (PTHR24073) (Fig 18), it may not be feasible to annotate all clades at the same time. In this kind of situation, you may choose to annotate only the clades you are knowledgeable and confident of, and leave other clades unexamined. When you do this, you should fully annotate the clades you choose to annotate. For example, if you choose to do the IFT27 clade, do it fully. Please don't do piecemeal annotations in various locations that may make it hard for a subsequent annotator to understand what has been done. <br />
<br />
We also agreed at the July 2014 PAINT Jamboree that you can make propagations all the way to the root if you feel that there is an ancestral role, even if you think that some clades have lost this. For example, in the RAB GTPase superfamily, we think that it had an ancestral function as a GTPase, but it is possible that some clades, e.g. the IFT22 clade, have lost this ancestral activity. You can make these high level propagations as part of your initial annotation of the family. If there are clades where this is wrong, perhaps the IBA annotation from PAINT will generate feedback that will help us correct it.<br />
<br />
=== Recording partial annotation in the notes file ===<br />
If you only partially annotate a tree, please record in the notes file which clades you have worked on using the node number, e.g. '''Eukaryota_PTN001180007''' as well as a common name, e.g. '''IFT27''', if it is helpful.<br />
<br />
==Recording trees examined, but not annotated==<br />
<br />
When you examine a tree and feel that it should not be annotated for some reason, please record that in the Evidence Notes so that we can track the fact that the family has been examined. Please use one of these tags (in all caps) in the Notes section of the Evidence tab. You can additional information after the tag if you wish (syntax between tag and additional info not discussed or determined). Then, save your annotations as normal so that PAINT will save the notes file.<br />
<br />
* '''MISSING ANNOTATION''' - Use this if the tree looks OK, but there are insufficient experimental annotations to propagate any annotations.<br />
* '''MISSING SEQUENCE''' - Use this if you feel that a specific sequence or sequences is missing. You can list the IDs of the sequence(s) after the tag.<br />
* '''BAD TREE''' - Use this if you feel that the tree has major problems beyond one or a few missing sequences.<br />
<br />
----<br />
=Interpreting the PANTHER trees=<br />
==Speciation and duplication events, and horizontal transfer==<br />
In the tree, a speciation node is shown with a circle, and a gene duplication node with an square. Horizontal transfer events also appear in the tree, though more rarely, and these are represented with a diamond.<br />
<br />
==Branch lengths==<br />
* Branch lengths show the amount of sequence divergence that has occurred between a given node and its ancestral node, in terms of the average number of amino acid substitutions per site. Shorter branches indicate less sequence divergence and therefore greater conservation of ancestral characters. A branch might be shorter because of a slower evolutionary rate (greater negative selection), or because less "time" has gone by (actually a combination of number of generations and population dynamics), or both.<br />
* Very long branches indicate an unreliable divergence estimate, due to insufficient data. Note that sometimes there is not enough data to compare all branches that descend from a given node. In this case, we have set all descendant branches to a length of 2.0 (very long branches). Branch lengths of 2.0 are often due to a sequence fragment, and at a duplication node it may also indicate a gene that has been incorrectly broken into two different genes by a gene prediction program.<br />
* Following a gene duplication (after a square node), the relative branch lengths for descendant branches are particularly useful: the shortest branch (least diverged) is more likely to have greater functional conservation.<br />
<br />
==Multiple sequence alignment (MSA)==<br />
* Some columns in the MSA have upper-case characters (and dashes '-' for insertions/deletions). These columns were used to estimate the phylogenetic tree.<br />
* Lower-case characters and periods (‘.’ for insertions/deletions) denote positions that were ignored when estimating the phylogenetic tree. Sometimes, tree errors arise because not enough columns were used, and the phylogeny could not be reconstructed well based on the included columns. Since they were not used in the phylogeny, lower-case characters can be particularly helpful in verifying the tree topology: any conserved insertions should be parsimoniously traceable to a common ancestor.<br />
<br />
----<br />
=Reporting bugs or likely errors in the trees=<br />
<br />
==Tree issues==<br />
Most often, the errors in phylogenetic trees are due to problems with the sequence alignment, or the specific MSA columns used to estimate the phylogeny. The phylogeny inference program performs fairly robust handling of sequence fragments, but sequence fragments still cause errors. Another source of error is when the sequences evolve very slowly, generating little variation from which to estimate phylogeny. In this case, the errors can usually be fixed by including additional alignment positions to consider in the phylogeny. <br />
<br />
'''If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues'''<br />
<br />
==PAINT issues==<br />
'''Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues'''<br />
<br />
=Curation Guidelines=<br />
<br />
'''Those guidelines have been published (Gaudet, Livestone, Lewis, Thomas, 2011) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059/?tool=pubmed]'''<br />
<br />
<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: 2021-07-01<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=20_September_2023_PAINT_Conference_Call&diff=8601720 September 2023 PAINT Conference Call2023-09-20T19:19:18Z<p>Mi: /* Shortening the cycle between new experimental annotations and PAINT */</p>
<hr />
<div>==Present==<br />
<br />
Pascale, Marc, Dustin, Anushya, Huaiyu, Paul<br />
<br />
==Agenda==<br />
<br />
===PANTHER17 tree review===<br />
Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH_CEuD79xWAjV5p4/edit#gid=0 spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.<br />
<br />
'''Minutes'''<br />
* Report on just annotations lost in migration due to obsoleted term ''even when there was a replacement term available''. (Dustin)<br />
* Find all IBDs that lost the annotation due to obsoleted term and add the replacement terms. This data, either loaded in the database or as a file, can be used for 18 migration.<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
'''Minutes'''<br />
The extensive discussions boil down to the following two GitHub tickets:<br />
* https://github.com/pantherdb/db-PAINT/issues/58<br />
* https://github.com/pantherdb/db-PAINT/issues/57<br />
We should continue the discussion within those tickets.<br />
<br />
===PANTHER18.0 release===<br />
PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.<br />
<br />
'''Minutes'''<br />
* It is related to the first item in the agenda.<br />
* Paul suggested to wait until v.19.0. However, the main variable about v.19 release is the update to generate alignment using MAFFT.<br />
* No decision was made.<br />
<br />
===S. japonicus taxon issue===<br />
See GitHub issue: https://github.com/japonicusdb/japonicus-curation/issues/57#issuecomment-1721024110<br />
<br />
Basically, Pombase extracts S. japonicus annotations from JaponicusDB with the species taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4897&lvl=3&keep=1&srchmode=1&unlock 4897], while PAINT uses the S. japonicus data from the Reference Proteome with a strain taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=402676&lvl=3&lin=f&keep=1&srchmode=1&unlock 402676]. The ticket is asking whether PAINT can support the species taxon ID.<br />
* We could retain RefProt's strain taxon in PAINT but use the strain->species taxon relationship in NCBITaxon ontology to export the species taxon in the GAF. Obviously, this would complicate the pipeline a bit.<br />
<br />
'''Minutes'''<br />
* We probably can't just replace the taxon ID in PAINT, because the genomes for the species (taxon:4897) and the strain (taxon:402676) are different, and therefore the sequence IDs can be different.<br />
* The proper fix is probably to ask Reference Proteome to switch from the strain to the species genome. Huaiyu will contact Maria about it.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=20_September_2023_PAINT_Conference_Call&diff=8601620 September 2023 PAINT Conference Call2023-09-20T18:45:35Z<p>Mi: /* S. japonicus taxon issue */</p>
<hr />
<div>==Present==<br />
<br />
Pascale, Marc, Dustin, Anushya, Huaiyu, Paul<br />
<br />
==Agenda==<br />
<br />
===PANTHER17 tree review===<br />
Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH_CEuD79xWAjV5p4/edit#gid=0 spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.<br />
<br />
'''Minutes'''<br />
* Report on just annotations lost in migration due to obsoleted term ''even when there was a replacement term available''. (Dustin)<br />
* Find all IBDs that lost the annotation due to obsoleted term and add the replacement terms. This data, either loaded in the database or as a file, can be used for 18 migration.<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
'''Minutes'''<br />
<br />
===PANTHER18.0 release===<br />
PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.<br />
<br />
'''Minutes'''<br />
* It is related to the first item in the agenda.<br />
* Paul suggested to wait until v.19.0. However, the main variable about v.19 release is the update to generate alignment using MAFFT.<br />
* No decision was made.<br />
<br />
===S. japonicus taxon issue===<br />
See GitHub issue: https://github.com/japonicusdb/japonicus-curation/issues/57#issuecomment-1721024110<br />
<br />
Basically, Pombase extracts S. japonicus annotations from JaponicusDB with the species taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4897&lvl=3&keep=1&srchmode=1&unlock 4897], while PAINT uses the S. japonicus data from the Reference Proteome with a strain taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=402676&lvl=3&lin=f&keep=1&srchmode=1&unlock 402676]. The ticket is asking whether PAINT can support the species taxon ID.<br />
* We could retain RefProt's strain taxon in PAINT but use the strain->species taxon relationship in NCBITaxon ontology to export the species taxon in the GAF. Obviously, this would complicate the pipeline a bit.<br />
<br />
'''Minutes'''<br />
* We probably can't just replace the taxon ID in PAINT, because the genomes for the species (taxon:4897) and the strain (taxon:402676) are different, and therefore the sequence IDs can be different.<br />
* The proper fix is probably to ask Reference Proteome to switch from the strain to the species genome. Huaiyu will contact Maria about it.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=20_September_2023_PAINT_Conference_Call&diff=8601520 September 2023 PAINT Conference Call2023-09-20T18:42:04Z<p>Mi: /* PANTHER18.0 release */</p>
<hr />
<div>==Present==<br />
<br />
Pascale, Marc, Dustin, Anushya, Huaiyu, Paul<br />
<br />
==Agenda==<br />
<br />
===PANTHER17 tree review===<br />
Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH_CEuD79xWAjV5p4/edit#gid=0 spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.<br />
<br />
'''Minutes'''<br />
* Report on just annotations lost in migration due to obsoleted term ''even when there was a replacement term available''. (Dustin)<br />
* Find all IBDs that lost the annotation due to obsoleted term and add the replacement terms. This data, either loaded in the database or as a file, can be used for 18 migration.<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
'''Minutes'''<br />
<br />
===PANTHER18.0 release===<br />
PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.<br />
<br />
'''Minutes'''<br />
* It is related to the first item in the agenda.<br />
* Paul suggested to wait until v.19.0. However, the main variable about v.19 release is the update to generate alignment using MAFFT.<br />
* No decision was made.<br />
<br />
===S. japonicus taxon issue===<br />
See GitHub issue: https://github.com/japonicusdb/japonicus-curation/issues/57#issuecomment-1721024110<br />
<br />
Basically, Pombase extracts S. japonicus annotations from JaponicusDB with the species taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4897&lvl=3&keep=1&srchmode=1&unlock 4897], while PAINT uses the S. japonicus data from the Reference Proteome with a strain taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=402676&lvl=3&lin=f&keep=1&srchmode=1&unlock 402676]. The ticket is asking whether PAINT can support the species taxon ID.<br />
* We could retain RefProt's strain taxon in PAINT but use the strain->species taxon relationship in NCBITaxon ontology to export the species taxon in the GAF. Obviously, this would complicate the pipeline a bit.<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=20_September_2023_PAINT_Conference_Call&diff=8601420 September 2023 PAINT Conference Call2023-09-20T18:40:02Z<p>Mi: /* PANTHER17 tree review */</p>
<hr />
<div>==Present==<br />
<br />
Pascale, Marc, Dustin, Anushya, Huaiyu, Paul<br />
<br />
==Agenda==<br />
<br />
===PANTHER17 tree review===<br />
Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH_CEuD79xWAjV5p4/edit#gid=0 spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.<br />
<br />
'''Minutes'''<br />
* Report on just annotations lost in migration due to obsoleted term ''even when there was a replacement term available''. (Dustin)<br />
* Find all IBDs that lost the annotation due to obsoleted term and add the replacement terms. This data, either loaded in the database or as a file, can be used for 18 migration.<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
'''Minutes'''<br />
<br />
===PANTHER18.0 release===<br />
PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.<br />
<br />
===S. japonicus taxon issue===<br />
See GitHub issue: https://github.com/japonicusdb/japonicus-curation/issues/57#issuecomment-1721024110<br />
<br />
Basically, Pombase extracts S. japonicus annotations from JaponicusDB with the species taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4897&lvl=3&keep=1&srchmode=1&unlock 4897], while PAINT uses the S. japonicus data from the Reference Proteome with a strain taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=402676&lvl=3&lin=f&keep=1&srchmode=1&unlock 402676]. The ticket is asking whether PAINT can support the species taxon ID.<br />
* We could retain RefProt's strain taxon in PAINT but use the strain->species taxon relationship in NCBITaxon ontology to export the species taxon in the GAF. Obviously, this would complicate the pipeline a bit.<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=20_September_2023_PAINT_Conference_Call&diff=8601320 September 2023 PAINT Conference Call2023-09-20T18:39:49Z<p>Mi: /* Shortening the cycle between new experimental annotations and PAINT */</p>
<hr />
<div>==Present==<br />
<br />
Pascale, Marc, Dustin, Anushya, Huaiyu, Paul<br />
<br />
==Agenda==<br />
<br />
===PANTHER17 tree review===<br />
Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH_CEuD79xWAjV5p4/edit#gid=0 spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.<br />
* Report on just annotations lost in migration due to obsoleted term ''even when there was a replacement term available''. (Dustin)<br />
* Find all IBDs that lost the annotation due to obsoleted term and add the replacement terms. This data, either loaded in the database or as a file, can be used for 18 migration.<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
'''Minutes'''<br />
<br />
===PANTHER18.0 release===<br />
PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.<br />
<br />
===S. japonicus taxon issue===<br />
See GitHub issue: https://github.com/japonicusdb/japonicus-curation/issues/57#issuecomment-1721024110<br />
<br />
Basically, Pombase extracts S. japonicus annotations from JaponicusDB with the species taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4897&lvl=3&keep=1&srchmode=1&unlock 4897], while PAINT uses the S. japonicus data from the Reference Proteome with a strain taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=402676&lvl=3&lin=f&keep=1&srchmode=1&unlock 402676]. The ticket is asking whether PAINT can support the species taxon ID.<br />
* We could retain RefProt's strain taxon in PAINT but use the strain->species taxon relationship in NCBITaxon ontology to export the species taxon in the GAF. Obviously, this would complicate the pipeline a bit.<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=20_September_2023_PAINT_Conference_Call&diff=8601220 September 2023 PAINT Conference Call2023-09-20T18:36:49Z<p>Mi: /* PANTHER17 tree review */</p>
<hr />
<div>==Present==<br />
<br />
Pascale, Marc, Dustin, Anushya, Huaiyu, Paul<br />
<br />
==Agenda==<br />
<br />
===PANTHER17 tree review===<br />
Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH_CEuD79xWAjV5p4/edit#gid=0 spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.<br />
* Report on just annotations lost in migration due to obsoleted term ''even when there was a replacement term available''. (Dustin)<br />
* Find all IBDs that lost the annotation due to obsoleted term and add the replacement terms. This data, either loaded in the database or as a file, can be used for 18 migration.<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
===PANTHER18.0 release===<br />
PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.<br />
<br />
===S. japonicus taxon issue===<br />
See GitHub issue: https://github.com/japonicusdb/japonicus-curation/issues/57#issuecomment-1721024110<br />
<br />
Basically, Pombase extracts S. japonicus annotations from JaponicusDB with the species taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4897&lvl=3&keep=1&srchmode=1&unlock 4897], while PAINT uses the S. japonicus data from the Reference Proteome with a strain taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=402676&lvl=3&lin=f&keep=1&srchmode=1&unlock 402676]. The ticket is asking whether PAINT can support the species taxon ID.<br />
* We could retain RefProt's strain taxon in PAINT but use the strain->species taxon relationship in NCBITaxon ontology to export the species taxon in the GAF. Obviously, this would complicate the pipeline a bit.<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=20_September_2023_PAINT_Conference_Call&diff=8601120 September 2023 PAINT Conference Call2023-09-20T16:30:33Z<p>Mi: /* Present */</p>
<hr />
<div>==Present==<br />
<br />
Pascale, Marc, Dustin, Anushya, Huaiyu, Paul<br />
<br />
==Agenda==<br />
<br />
===PANTHER17 tree review===<br />
Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH_CEuD79xWAjV5p4/edit#gid=0 spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.<br />
* Report on just annotations lost in migration due to obsoleted term ''even when there was a replacement term available''. (Dustin)<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
===PANTHER18.0 release===<br />
PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.<br />
<br />
===S. japonicus taxon issue===<br />
See GitHub issue: https://github.com/japonicusdb/japonicus-curation/issues/57#issuecomment-1721024110<br />
<br />
Basically, Pombase extracts S. japonicus annotations from JaponicusDB with the species taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4897&lvl=3&keep=1&srchmode=1&unlock 4897], while PAINT uses the S. japonicus data from the Reference Proteome with a strain taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=402676&lvl=3&lin=f&keep=1&srchmode=1&unlock 402676]. The ticket is asking whether PAINT can support the species taxon ID.<br />
* We could retain RefProt's strain taxon in PAINT but use the strain->species taxon relationship in NCBITaxon ontology to export the species taxon in the GAF. Obviously, this would complicate the pipeline a bit.<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=20_September_2023_PAINT_Conference_Call&diff=8597620 September 2023 PAINT Conference Call2023-09-15T16:41:16Z<p>Mi: </p>
<hr />
<div>==Present==<br />
<br />
<br />
<br />
==Agenda==<br />
<br />
===PANTHER17 tree review===<br />
Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH%20CEuD79xWAjV5p4/edit spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.<br />
<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
===PANTHER18.0 release===<br />
PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.<br />
<br />
===S. japonicus taxon issue===<br />
See GitHub issue: https://github.com/japonicusdb/japonicus-curation/issues/57#issuecomment-1721024110<br />
<br />
Basically, Pombase extracts S. japonicus annotations from JaponicusDB with the species taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4897&lvl=3&keep=1&srchmode=1&unlock 4897], while PAINT uses the S. japonicus data from the Reference Proteome with a strain taxon ID [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=402676&lvl=3&lin=f&keep=1&srchmode=1&unlock 402676]. The ticket is asking whether PAINT can support the species taxon ID.<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=20_September_2023_PAINT_Conference_Call&diff=8592820 September 2023 PAINT Conference Call2023-09-12T16:51:36Z<p>Mi: Created page with "==Present== ==Agenda== ===PANTHER17 tree review=== Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH%20CEuD79xWAjV5p4/edit spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term. ===Shortening the cycle between new experimental annotations and PAINT=== Currently, once new experimental annotations are rele..."</p>
<hr />
<div>==Present==<br />
<br />
<br />
<br />
==Agenda==<br />
<br />
===PANTHER17 tree review===<br />
Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH%20CEuD79xWAjV5p4/edit spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term.<br />
<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
===PANTHER18.0 release===<br />
PANTHER18.0 will be released this month. We need to determine when to release it to PAINT.<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_Conference_Calls&diff=85927PAINT Conference Calls2023-09-12T16:44:11Z<p>Mi: </p>
<hr />
<div>[[Category:Reference Genome]][[Category:Archived]]<br />
The second Wednesday of each month; 9 AM Pacific time<br />
<br />
==PAINT Conference Call Agenda and Minutes 2023== <br />
* [[1 Feb 2023_PAINT_Conference_Call]]<br />
* [[1 March 2023_PAINT_Conference_Call]]<br />
* [[12 April 2023_PAINT_Conference_Call]]<br />
* [[17 May 2023_PAINT_Conference_Call]]<br />
* [[14 June 2023_PAINT_Conference_Call]]<br />
* [[20 September 2023_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2022== <br />
* [[8 Feb 2022_PAINT_Conference_Call]]<br />
* [[20 Apr 2022_PAINT_Conference_Call]]<br />
* [[6th July 2022_PAINT_Conference_Call]]<br />
* [[3rd Aug 2022_PAINT_Conference_call]]<br />
* [[7th Sept 2022_PAINT_Conference_call]]<br />
* [[5th Oct 2022_PAINT_Conference_call]]<br />
* [[2nd Nov 2022_PAINT_Conference_call]]<br />
* [[7th Dec 2022_PAINT_Conference_call]]<br />
<br />
==PAINT Conference Call Minutes 2021== <br />
* [[5 Jan 2021_PAINT_Conference_Call]]<br />
* [[26 Jan 2021_PAINT_Conference_Call]]<br />
* [[2 Mar 2021_PAINT_Conference_Call]]<br />
* [[6 Apr 2021_PAINT_Conference_Call]]<br />
* [[27 Apr 2021_PAINT_Conference_Call]] (since May 4th is the GO meeting)<br />
* [[1 Jun 2021_PAINT_Conference_Call]]<br />
* [[6 Jul 2021_PAINT_Conference_Call]]<br />
* [[3 Aug 2021_PAINT_Conference_Call]]<br />
* [[31 Aug 2021_PAINT_Conference_Call]]<br />
* [[5 Oct 2021_PAINT_Conference_Call]]<br />
* [[2 Nov 2021_PAINT_Conference_Call]]<br />
* [[7 Dec 2021_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2020== <br />
* [[7 Jan 2020_PAINT_Conference_Call]]<br />
* [[4 Fev 2020_PAINT_Conference_Call]]<br />
* [[3 March 2020_PAINT_Conference_Call]]<br />
* [[7 April 2020_PAINT_Conference_Call]]<br />
* [[5 May 2020_PAINT_Conference_Call]]<br />
* [[2 June 2020_PAINT_Conference_Call]]<br />
* [[7 July 2020_PAINT_Conference_Call]]<br />
* [[1 September 2020_PAINT_Conference_Call]]<br />
* [[6 October 2020_PAINT_Conference_Call]]<br />
* [[10 November 2020_PAINT_Conference_Call]]<br />
* [[1 December 2020_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2019== <br />
* [[5 March 2019_PAINT_Conference_Call]]<br />
* [[2 April 2019_PAINT_Conference_Call]]<br />
* [[7 May 2019_PAINT_Conference_Call]]<br />
* [[4 June 2019_PAINT_Conference_Call]]<br />
* [[9 July 2019_PAINT_Conference_Call]]<br />
* [[13 August 2019_PAINT_Conference_Call]]<br />
* [[3 September 2019_PAINT_Conference_Call]]<br />
* [[1 October 2019_PAINT_Conference_Call]]<br />
* [[5 November 2019_PAINT_Conference_Call]]<br />
* [[3 December 2019_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2016== <br />
* [[19 January 2016_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call Minutes 2015== <br />
* [[1 December 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 November 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[21 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[16 June 2015_PAINT_Conference_call]] 8 AM Pacific<br />
* [[2 June 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[19 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[5 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 April 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 3 PM UK<br />
* [[3 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[3 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call minutes Minutes 2014==<br />
<br />
* [[16 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[2 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[23 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[9 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[26 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[12 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[8 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[24 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[10 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[13 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[1 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[25 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[11 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[25 FEB 2014_PAINT_Phone_Conference_call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[11 FEB 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[28 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[14 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2013==<br />
<br />
<br />
* [[13 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2011==<br />
* [[14 JUNE 2011_RefGen_Phone_Conference]] 8 AM Pacific, 10 AM Central, 11 AM Eastern, 4 PM UK<br />
* [[10 MAY 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[12 APR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 MAR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 FEB 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 JAN 2011_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 DEC 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
<br />
==PAINT Conference Call minutes Minutes 2010==<br />
* [[9 NOV 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* OCT 2010 CANCELED - Conflict with the Biocuration meeting<br />
* [[28 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[21 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[14 SEPT 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[10 AUG 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[13 JULY 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[8 JUN 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 MAY 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* 13 APR 2010_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[9 MAR 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[9 FEB 2010_RefGen_Phone_Conference]] 8 AM PST, 10 AM CST, 11 AM EST, 4 PM BST<br />
* [[12 JAN 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2009==<br />
* 8 Dec 2009_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[10 NOV 2009_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[13 Oct 2009_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[8 Sept 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 July 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[9 June 2009_RefGen_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
* 12May2009_RefGen_Phone_Conference CANCELED, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
*14April2009_RefGen_Phone_Conference: CANCELED, 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
*[[10March09_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 6 PM BST** Time not changed yet)<br />
*[[RefGenome10Feb09_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*RefGenome13Jan09_Phone_Conference: CANCELED<br />
<br />
==PAINT Conference Call minutes Minutes 2008==<br />
*[[RefGenome9Dec08_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*[[RefGenome11Nov08_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST)<br />
* RefGenome14Oct08_Phone_Conference: CANCELED<br />
*[[RefGenome9Sept08_Phone_Conference]]<br />
*[[RefGenome12Aug08_Phone_Conference]]<br />
*[[RefGenome8Jul08_Phone_Conference]]<br />
*[[RefGenome10Jun08_Phone_Conference]]<br />
*RefGenome13May08_Phone_Conference CANCELED<br />
*[[RefGenome8Apr08_Phone_Conference]]<br />
*[[RefGenome11Mar08_Phone_Conference]]<br />
*[[RefGenome12Feb08_Phone_Conference]]<br />
*[[RefGenome08Jan08_Phone_Conference]]<br />
<br />
==PAINT Conference Call minutes Minutes 2007==<br />
*[[RefGenome11Dec07_Phone_Conference]]<br />
*[[RefGenome13Nov07_Phone_Conference]]<br />
*[[RefGenome9Oct07_Phone_Conference]]<br />
*[[RefGenome11Sept07_Phone_Conference]]<br />
*[[RefGenome07Aug07_Phone_Conference]]<br />
*[[RefGenome10July07_Phone_Conference]]<br />
*[[RefGenome12Jun07_Phone_Conference]]<br />
<br />
<br />
<br />
[[Phylogenetic_Annotation_Project | Back to Phylogenetic Annotation Main Page]]</div>Mihttps://wiki.geneontology.org/index.php?title=13_September_2023_PAINT_Conference_Call&diff=8574213 September 2023 PAINT Conference Call2023-07-31T16:32:51Z<p>Mi: Created page with "==Present== ==Agenda== ===Shortening the cycle between new experimental annotations and PAINT=== Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas. *Snapshot is loaded weekly. *Noctua annotations could be loaded directly. *Literature curation is done directly in PAINT. Category:PAINT"</p>
<hr />
<div>==Present==<br />
<br />
<br />
<br />
==Agenda==<br />
<br />
===Shortening the cycle between new experimental annotations and PAINT===<br />
Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas.<br />
*Snapshot is loaded weekly.<br />
*Noctua annotations could be loaded directly.<br />
*Literature curation is done directly in PAINT.<br />
<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_Conference_Calls&diff=85741PAINT Conference Calls2023-07-31T16:24:55Z<p>Mi: /* PAINT Conference Call Agenda and Minutes 2023 */</p>
<hr />
<div>[[Category:Reference Genome]][[Category:Archived]]<br />
The second Wednesday of each month; 9 AM Pacific time<br />
<br />
==PAINT Conference Call Agenda and Minutes 2023== <br />
* [[1 Feb 2023_PAINT_Conference_Call]]<br />
* [[1 March 2023_PAINT_Conference_Call]]<br />
* [[12 April 2023_PAINT_Conference_Call]]<br />
* [[17 May 2023_PAINT_Conference_Call]]<br />
* [[14 June 2023_PAINT_Conference_Call]]<br />
* [[13 September 2023_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2022== <br />
* [[8 Feb 2022_PAINT_Conference_Call]]<br />
* [[20 Apr 2022_PAINT_Conference_Call]]<br />
* [[6th July 2022_PAINT_Conference_Call]]<br />
* [[3rd Aug 2022_PAINT_Conference_call]]<br />
* [[7th Sept 2022_PAINT_Conference_call]]<br />
* [[5th Oct 2022_PAINT_Conference_call]]<br />
* [[2nd Nov 2022_PAINT_Conference_call]]<br />
* [[7th Dec 2022_PAINT_Conference_call]]<br />
<br />
==PAINT Conference Call Minutes 2021== <br />
* [[5 Jan 2021_PAINT_Conference_Call]]<br />
* [[26 Jan 2021_PAINT_Conference_Call]]<br />
* [[2 Mar 2021_PAINT_Conference_Call]]<br />
* [[6 Apr 2021_PAINT_Conference_Call]]<br />
* [[27 Apr 2021_PAINT_Conference_Call]] (since May 4th is the GO meeting)<br />
* [[1 Jun 2021_PAINT_Conference_Call]]<br />
* [[6 Jul 2021_PAINT_Conference_Call]]<br />
* [[3 Aug 2021_PAINT_Conference_Call]]<br />
* [[31 Aug 2021_PAINT_Conference_Call]]<br />
* [[5 Oct 2021_PAINT_Conference_Call]]<br />
* [[2 Nov 2021_PAINT_Conference_Call]]<br />
* [[7 Dec 2021_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2020== <br />
* [[7 Jan 2020_PAINT_Conference_Call]]<br />
* [[4 Fev 2020_PAINT_Conference_Call]]<br />
* [[3 March 2020_PAINT_Conference_Call]]<br />
* [[7 April 2020_PAINT_Conference_Call]]<br />
* [[5 May 2020_PAINT_Conference_Call]]<br />
* [[2 June 2020_PAINT_Conference_Call]]<br />
* [[7 July 2020_PAINT_Conference_Call]]<br />
* [[1 September 2020_PAINT_Conference_Call]]<br />
* [[6 October 2020_PAINT_Conference_Call]]<br />
* [[10 November 2020_PAINT_Conference_Call]]<br />
* [[1 December 2020_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2019== <br />
* [[5 March 2019_PAINT_Conference_Call]]<br />
* [[2 April 2019_PAINT_Conference_Call]]<br />
* [[7 May 2019_PAINT_Conference_Call]]<br />
* [[4 June 2019_PAINT_Conference_Call]]<br />
* [[9 July 2019_PAINT_Conference_Call]]<br />
* [[13 August 2019_PAINT_Conference_Call]]<br />
* [[3 September 2019_PAINT_Conference_Call]]<br />
* [[1 October 2019_PAINT_Conference_Call]]<br />
* [[5 November 2019_PAINT_Conference_Call]]<br />
* [[3 December 2019_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2016== <br />
* [[19 January 2016_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call Minutes 2015== <br />
* [[1 December 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 November 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[21 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[16 June 2015_PAINT_Conference_call]] 8 AM Pacific<br />
* [[2 June 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[19 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[5 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 April 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 3 PM UK<br />
* [[3 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[3 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call minutes Minutes 2014==<br />
<br />
* [[16 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[2 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[23 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[9 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[26 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[12 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[8 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[24 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[10 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[13 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[1 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[25 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[11 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[25 FEB 2014_PAINT_Phone_Conference_call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[11 FEB 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[28 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[14 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2013==<br />
<br />
<br />
* [[13 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2011==<br />
* [[14 JUNE 2011_RefGen_Phone_Conference]] 8 AM Pacific, 10 AM Central, 11 AM Eastern, 4 PM UK<br />
* [[10 MAY 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[12 APR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 MAR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 FEB 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 JAN 2011_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 DEC 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
<br />
==PAINT Conference Call minutes Minutes 2010==<br />
* [[9 NOV 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* OCT 2010 CANCELED - Conflict with the Biocuration meeting<br />
* [[28 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[21 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[14 SEPT 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[10 AUG 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[13 JULY 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[8 JUN 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 MAY 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* 13 APR 2010_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[9 MAR 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[9 FEB 2010_RefGen_Phone_Conference]] 8 AM PST, 10 AM CST, 11 AM EST, 4 PM BST<br />
* [[12 JAN 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2009==<br />
* 8 Dec 2009_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[10 NOV 2009_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[13 Oct 2009_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[8 Sept 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 July 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[9 June 2009_RefGen_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
* 12May2009_RefGen_Phone_Conference CANCELED, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
*14April2009_RefGen_Phone_Conference: CANCELED, 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
*[[10March09_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 6 PM BST** Time not changed yet)<br />
*[[RefGenome10Feb09_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*RefGenome13Jan09_Phone_Conference: CANCELED<br />
<br />
==PAINT Conference Call minutes Minutes 2008==<br />
*[[RefGenome9Dec08_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*[[RefGenome11Nov08_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST)<br />
* RefGenome14Oct08_Phone_Conference: CANCELED<br />
*[[RefGenome9Sept08_Phone_Conference]]<br />
*[[RefGenome12Aug08_Phone_Conference]]<br />
*[[RefGenome8Jul08_Phone_Conference]]<br />
*[[RefGenome10Jun08_Phone_Conference]]<br />
*RefGenome13May08_Phone_Conference CANCELED<br />
*[[RefGenome8Apr08_Phone_Conference]]<br />
*[[RefGenome11Mar08_Phone_Conference]]<br />
*[[RefGenome12Feb08_Phone_Conference]]<br />
*[[RefGenome08Jan08_Phone_Conference]]<br />
<br />
==PAINT Conference Call minutes Minutes 2007==<br />
*[[RefGenome11Dec07_Phone_Conference]]<br />
*[[RefGenome13Nov07_Phone_Conference]]<br />
*[[RefGenome9Oct07_Phone_Conference]]<br />
*[[RefGenome11Sept07_Phone_Conference]]<br />
*[[RefGenome07Aug07_Phone_Conference]]<br />
*[[RefGenome10July07_Phone_Conference]]<br />
*[[RefGenome12Jun07_Phone_Conference]]<br />
<br />
<br />
<br />
[[Phylogenetic_Annotation_Project | Back to Phylogenetic Annotation Main Page]]</div>Mihttps://wiki.geneontology.org/index.php?title=14_June_2023_PAINT_Conference_Call&diff=8548014 June 2023 PAINT Conference Call2023-06-12T21:54:25Z<p>Mi: Created page with "==Present== Marc, Dustin, Anushya, Paul T, Huaiyu, Pascale ==Agenda== ===PANTHER 18 build=== The node forward tracking from v.15 to v.18 is not better than that from v.15 to 17. After more careful review of trees, the conclusion from the last call that trees map better from 15 to 18 is not true either. It seems that the differences in tree topology were caused by the sequence alignment. <Dustin, please add some stats here> Here is the proposed plan based on these dat..."</p>
<hr />
<div>==Present==<br />
Marc, Dustin, Anushya, Paul T, Huaiyu, Pascale<br />
<br />
<br />
==Agenda==<br />
<br />
===PANTHER 18 build===<br />
The node forward tracking from v.15 to v.18 is not better than that from v.15 to 17. After more careful review of trees, the conclusion from the last call that trees map better from 15 to 18 is not true either. It seems that the differences in tree topology were caused by the sequence alignment.<br />
<Dustin, please add some stats here><br />
<br />
Here is the proposed plan based on these data.<br />
* Continue to review families in PANTHER17.0.<br />
* We will test ways to keep the alignment more stable in future PANTHER builds, probably starting in PANTHER19.0.<br />
<br />
<br />
===PAN-GO paper===<br />
Status update. What remains to be do?<br />
https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=PAINT_Conference_Calls&diff=85479PAINT Conference Calls2023-06-12T20:30:20Z<p>Mi: /* PAINT Conference Call Agenda and Minutes 2023 */</p>
<hr />
<div>[[Category:Reference Genome]][[Category:Archived]]<br />
The second Wednesday of each month; 9 AM Pacific time<br />
<br />
==PAINT Conference Call Agenda and Minutes 2023== <br />
* [[1 Feb 2023_PAINT_Conference_Call]]<br />
* [[1 March 2023_PAINT_Conference_Call]]<br />
* [[12 April 2023_PAINT_Conference_Call]]<br />
* [[17 May 2023_PAINT_Conference_Call]]<br />
* [[14 June 2023_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2022== <br />
* [[8 Feb 2022_PAINT_Conference_Call]]<br />
* [[20 Apr 2022_PAINT_Conference_Call]]<br />
* [[6th July 2022_PAINT_Conference_Call]]<br />
* [[3rd Aug 2022_PAINT_Conference_call]]<br />
* [[7th Sept 2022_PAINT_Conference_call]]<br />
* [[5th Oct 2022_PAINT_Conference_call]]<br />
* [[2nd Nov 2022_PAINT_Conference_call]]<br />
* [[7th Dec 2022_PAINT_Conference_call]]<br />
<br />
==PAINT Conference Call Minutes 2021== <br />
* [[5 Jan 2021_PAINT_Conference_Call]]<br />
* [[26 Jan 2021_PAINT_Conference_Call]]<br />
* [[2 Mar 2021_PAINT_Conference_Call]]<br />
* [[6 Apr 2021_PAINT_Conference_Call]]<br />
* [[27 Apr 2021_PAINT_Conference_Call]] (since May 4th is the GO meeting)<br />
* [[1 Jun 2021_PAINT_Conference_Call]]<br />
* [[6 Jul 2021_PAINT_Conference_Call]]<br />
* [[3 Aug 2021_PAINT_Conference_Call]]<br />
* [[31 Aug 2021_PAINT_Conference_Call]]<br />
* [[5 Oct 2021_PAINT_Conference_Call]]<br />
* [[2 Nov 2021_PAINT_Conference_Call]]<br />
* [[7 Dec 2021_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2020== <br />
* [[7 Jan 2020_PAINT_Conference_Call]]<br />
* [[4 Fev 2020_PAINT_Conference_Call]]<br />
* [[3 March 2020_PAINT_Conference_Call]]<br />
* [[7 April 2020_PAINT_Conference_Call]]<br />
* [[5 May 2020_PAINT_Conference_Call]]<br />
* [[2 June 2020_PAINT_Conference_Call]]<br />
* [[7 July 2020_PAINT_Conference_Call]]<br />
* [[1 September 2020_PAINT_Conference_Call]]<br />
* [[6 October 2020_PAINT_Conference_Call]]<br />
* [[10 November 2020_PAINT_Conference_Call]]<br />
* [[1 December 2020_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2019== <br />
* [[5 March 2019_PAINT_Conference_Call]]<br />
* [[2 April 2019_PAINT_Conference_Call]]<br />
* [[7 May 2019_PAINT_Conference_Call]]<br />
* [[4 June 2019_PAINT_Conference_Call]]<br />
* [[9 July 2019_PAINT_Conference_Call]]<br />
* [[13 August 2019_PAINT_Conference_Call]]<br />
* [[3 September 2019_PAINT_Conference_Call]]<br />
* [[1 October 2019_PAINT_Conference_Call]]<br />
* [[5 November 2019_PAINT_Conference_Call]]<br />
* [[3 December 2019_PAINT_Conference_Call]]<br />
<br />
==PAINT Conference Call Minutes 2016== <br />
* [[19 January 2016_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call Minutes 2015== <br />
* [[1 December 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 November 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 October 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 August 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[21 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 July 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[16 June 2015_PAINT_Conference_call]] 8 AM Pacific<br />
* [[2 June 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[19 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[5 May 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[7 April 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 3 PM UK<br />
* [[3 March 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[17 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[3 Feburary 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[20 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[6 January 2015_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
<br />
==PAINT Conference Call minutes Minutes 2014==<br />
<br />
* [[16 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[2 December 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[18 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[4 November 2014_PAINT_Conference_Call]] 8 AM Pacific, 10 AM Central, 11 PM Eastern, 4 PM UK<br />
* [[23 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[9 September 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[26 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[12 August 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[8 July 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[24 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[10 June 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[13 May 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[22 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[1 APR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[25 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[11 MAR 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 4 PM UK<br />
* [[25 FEB 2014_PAINT_Phone_Conference_call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[11 FEB 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[28 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[14 JAN 2014_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2013==<br />
<br />
<br />
* [[13 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
* [[27 AUG 2013_PAINT_Conference_Call]] 9 AM Pacific, 11 AM Central, 12 PM Eastern, 5 PM UK<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2011==<br />
* [[14 JUNE 2011_RefGen_Phone_Conference]] 8 AM Pacific, 10 AM Central, 11 AM Eastern, 4 PM UK<br />
* [[10 MAY 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[12 APR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 MAR 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[08 FEB 2011_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 JAN 2011_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 DEC 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
<br />
==PAINT Conference Call minutes Minutes 2010==<br />
* [[9 NOV 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* OCT 2010 CANCELED - Conflict with the Biocuration meeting<br />
* [[28 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[21 SEPT 2010 RefGen Priorities Discussion]]<br />
* [[14 SEPT 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[10 AUG 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[13 JULY 2010_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[8 JUN 2010_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[11 MAY 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* 13 APR 2010_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[9 MAR 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[9 FEB 2010_RefGen_Phone_Conference]] 8 AM PST, 10 AM CST, 11 AM EST, 4 PM BST<br />
* [[12 JAN 2010_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
<br />
<br />
==PAINT Conference Call minutes Minutes 2009==<br />
* 8 Dec 2009_RefGen_Phone_Conference CANCELED 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[10 NOV 2009_RefGen_Phone_Conference]] 11 AM PST, 1 PM CST, 2 PM EST, 7 PM BST<br />
* [[13 Oct 2009_RefGen_Phone_Conference]] 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
* [[8 Sept 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[14 July 2009_RefGen_Phone_Conference]] 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
* [[9 June 2009_RefGen_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
* 12May2009_RefGen_Phone_Conference CANCELED, 11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST<br />
*14April2009_RefGen_Phone_Conference: CANCELED, 8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST<br />
*[[10March09_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 6 PM BST** Time not changed yet)<br />
*[[RefGenome10Feb09_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*RefGenome13Jan09_Phone_Conference: CANCELED<br />
<br />
==PAINT Conference Call minutes Minutes 2008==<br />
*[[RefGenome9Dec08_Phone_Conference]] (8 AM PDT, 10 AM CDT, 11 AM EST, 4 PM BST)<br />
*[[RefGenome11Nov08_Phone_Conference]] (11 AM PDT, 1 PM CDT, 2 PM EST, 7 PM BST)<br />
* RefGenome14Oct08_Phone_Conference: CANCELED<br />
*[[RefGenome9Sept08_Phone_Conference]]<br />
*[[RefGenome12Aug08_Phone_Conference]]<br />
*[[RefGenome8Jul08_Phone_Conference]]<br />
*[[RefGenome10Jun08_Phone_Conference]]<br />
*RefGenome13May08_Phone_Conference CANCELED<br />
*[[RefGenome8Apr08_Phone_Conference]]<br />
*[[RefGenome11Mar08_Phone_Conference]]<br />
*[[RefGenome12Feb08_Phone_Conference]]<br />
*[[RefGenome08Jan08_Phone_Conference]]<br />
<br />
==PAINT Conference Call minutes Minutes 2007==<br />
*[[RefGenome11Dec07_Phone_Conference]]<br />
*[[RefGenome13Nov07_Phone_Conference]]<br />
*[[RefGenome9Oct07_Phone_Conference]]<br />
*[[RefGenome11Sept07_Phone_Conference]]<br />
*[[RefGenome07Aug07_Phone_Conference]]<br />
*[[RefGenome10July07_Phone_Conference]]<br />
*[[RefGenome12Jun07_Phone_Conference]]<br />
<br />
<br />
<br />
[[Phylogenetic_Annotation_Project | Back to Phylogenetic Annotation Main Page]]</div>Mihttps://wiki.geneontology.org/index.php?title=17_May_2023_PAINT_Conference_Call&diff=8534617 May 2023 PAINT Conference Call2023-05-18T01:01:13Z<p>Mi: /* PANTHER 18 build */</p>
<hr />
<div>==Present==<br />
Marc, Dustin, Anushya, Paul T, Huaiyu, Pascale<br />
<br />
<br />
==Agenda==<br />
<br />
===Dropping mouse and rat IMP annotations from the PAINT load (by Pascale)===<br />
<br />
*Marc found that families with genes involved in immune response have a large number of IMP annotations that are usually not accurate. These annotations affect the efficiency in paint curation.<br />
*The decision is to still load all experimental annotations to the PAINT data. The PAINT tool will be modified to display an evidence code filter page so that the curator can select experimental annotations with specific code to display. The matrix will only show the experimental annotation with selected ECs. Annotations with unselected ECs will not be included in the matrix.<br />
<br />
===PANTHER 18 build===<br />
Node forward tracking comparisons<br />
* 15.0 -> 18.0<br />
** LEAF - 1776325 / 1968819 = 90.2%<br />
** SPECIATION - 1073649 / 1138527 = 94.3% <br />
** DUPLICATION - 291797 / 367319 = 79.4%<br />
** HORIZONTAL TRANSFER - 5185 / 6838 = 75.8%<br />
** ALL - 3146956<br />
* 15.0 -> 17.0<br />
** LEAF - 1847433 / 1973248 = 93.6%<br />
** SPECIATION - 1025670 / 1137262 = 90.1%<br />
** DUPLICATION - 299119 / 371052 = 80.6%<br />
** HORIZONTAL TRANSFER - 4436 / 6973 = 63.6%<br />
** ALL - 3176658<br />
* 17.0 -> 18.0<br />
** TODO (Coming soon!)<br />
<br />
Based on the review of some trees, it seems that the v18 trees are more similar to v15 trees, which is consistent with the results above. <br />
* It seems that the trees map better from 15 to 18, pending results from 17 to 18 mapping. If that is the case, it makes more sense that we will migrate PAINT annotations from 15 to 17.<br />
* We will pause annotation review and curation in v17. <br />
* We will continue to gather results, especially the v17 to 18 map. We will also review more trees. A decision will be made based the results, probably in two weeks.<br />
<br />
===PAN-GO paper===<br />
Status update. What remains to be do?<br />
<br />
<br />
[[Category:PAINT]]</div>Mihttps://wiki.geneontology.org/index.php?title=17_May_2023_PAINT_Conference_Call&diff=8534517 May 2023 PAINT Conference Call2023-05-18T00:46:46Z<p>Mi: /* Dropping mouse and rat IMP annotations from the PAINT load (by Pascale) */</p>
<hr />
<div>==Present==<br />
Marc, Dustin, Anushya, Paul T, Huaiyu, Pascale<br />
<br />
<br />
==Agenda==<br />
<br />
===Dropping mouse and rat IMP annotations from the PAINT load (by Pascale)===<br />
<br />
*Marc found that families with genes involved in immune response have a large number of IMP annotations that are usually not accurate. These annotations affect the efficiency in paint curation.<br />
*The decision is to still load all experimental annotations to the PAINT data. The PAINT tool will be modified to display an evidence code filter page so that the curator can select experimental annotations with specific code to display. The matrix will only show the experimental annotation with selected ECs. Annotations with unselected ECs will not be included in the matrix.<br />
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===PANTHER 18 build===<br />
Node forward tracking comparisons<br />
* 15.0 -> 18.0<br />
** LEAF - 1776325 / 1968819 = 90.2%<br />
** SPECIATION - 1073649 / 1138527 = 94.3% <br />
** DUPLICATION - 291797 / 367319 = 79.4%<br />
** HORIZONTAL TRANSFER - 5185 / 6838 = 75.8%<br />
** ALL - 3146956<br />
* 15.0 -> 17.0<br />
** LEAF - 1847433 / 1973248 = 93.6%<br />
** SPECIATION - 1025670 / 1137262 = 90.1%<br />
** DUPLICATION - 299119 / 371052 = 80.6%<br />
** HORIZONTAL TRANSFER - 4436 / 6973 = 63.6%<br />
** ALL - 3176658<br />
* 17.0 -> 18.0<br />
** TODO (Coming soon!)<br />
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===PAN-GO paper===<br />
Status update. What remains to be do?<br />
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[[Category:PAINT]]</div>Mi