Annotation Conf. Call, February 11, 2014: Difference between revisions

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[[Category:Annotation Working Group]]
==Agenda==
==Agenda==
Present:<br>
SGD: Rama, Diane, Paul<br>
MGI:David, Li<br>
EBI- Paola, Rachael, Pablo<br>
WB- Kimberley<br>
Dicty- Petra, Pascale<br>
Berkeley: Moni<br>
UCL: Ruth, Paul and Ana<br>


===Review of apoptosis related genes (Pascale)===
===Review of apoptosis related genes (Pascale)===
http://wiki.geneontology.org/index.php/PAINT_-_Apoptosis
http://wiki.geneontology.org/index.php/PAINT_-_Apoptosis


===QA checks (Rachael, Heiko)===
===QA checks in UniProt and Jenkins (Rachael)===
Tony sent Heiko (copied here) details of all the checks we do on our annotation sets with a view to including our checks if they were missing from Jenkins. It would be good to know how far along this is and if there are checks that cannot be included in Jenkins but that UniProt-GOA does have checks for.
 
There are checks that are not included in Jenkins but that UniProt-GOA does have checks for.


As far as I can see from the validation report, Jenkins checks for obsolete relations and checks GO terms in annotation extensions, but does it check for appropriate use of relations, e.g. if an entity type is out of range? Does it check for orphan ISS?
Jenkins checks for obsolete relations and checks GO terms in annotation extensions, but does it check for appropriate use of relations, e.g. if an entity type is out of range? Does it check for orphan ISS?


If Jenkins can't incorporate these checks, are groups interested in UniProt sending each group an error log for their annotations?
If Jenkins can't incorporate these checks, are groups interested in UniProt sending each group an error log for their annotations?
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but the UniProt-GOA check brings up several errors in 'domain/range';
but the UniProt-GOA check brings up several errors in 'domain/range';
<pre>
e.g.
e.g.
[[GO:0005829] [happens_during(GO:0034605)] [Invalid domain for happens_during: GO:0005829]]
[[GO:0005829] [happens_during(GO:0034605)] [Invalid domain for happens_during: GO:0005829]]
[[GO:1990188] [not_dependent_on(PomBase:SPCC736.11),occurs_at(SO:0001843)] [Invalid range for occurs_at: SO:0001843]]
[[GO:1990188] [not_dependent_on(PomBase:SPCC736.11),occurs_at(SO:0001843)] [Invalid range for occurs_at: SO:0001843]]
[[GO:1990188] [not_dependent_on(PomBase:SPCC736.11),occurs_at(SO:0001843)] [Invalid range for occurs_at: SO:0001843]]
[[GO:1990188] [not_dependent_on(PomBase:SPCC736.11),occurs_at(SO:0001843)] [Invalid range for occurs_at: SO:0001843]]
</pre>


Heiko, would you be available to give an update on this?
ACTION:
 
We will add rules to GO rule xml file
 
* http://www.geneontology.org/GO.annotation_qc.shtml -- User view
* http://www.geneontology.org/quality_control/annotation_checks/annotation_qc.xml -- source


===Coming soon===
===Coming soon===
* Feb 24th: David OS will talk about formalizing the representation of symbiotic relationships and annotations to describe them in the ontology
* Feb 24th: David OS will talk about formalizing the representation of symbiotic relationships and annotations to describe them in the ontology
* March 11th: Sandra Orchard will talk about the IntAct Complex portal
** GO annotations include many that involve an interaction between two organisms.  These include:<br>
annotation to a cell component of the host of the organisms expressing the gene being annotated.
annotation to a biological process involving a virus and and its host.
 
In these cases we have a mechanism for recording  multiple taxon IDs for interacting organisms, but not the relationship between the two organisms , e.g one might be host to the other or vector for the other.  We also don't have a way to record which of the two interacting organisms a cell component is located in or a biological process is occurring in.
 
My proposal aims to solve this problem, by allowing annotators to link taxon IDs using a relationship such as host_of or vector_for.  Additionally you will be able to use annotation extension to record which of the two organisms an annotated CC is located in or a biological process occurs in.
 
Along with this extension to annotation, I plan to rearrange parts of the CC hierarchy - particularly those relating to host cell.  My presentation will include details of these changes.
 
* TBA: Sandra Orchard will talk about the IntAct Complex portal
 
==Discussion==
===Apoptosis===
* lot of annotations moved upstream. Assay read out and the process involved are different. Paola has added comments to terms where applicable to clarify.
 
<pre>
1) A term with detailed annotation guidance and general annotation examples:
GO:0097527 necroptotic signaling pathway
(http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0097527)
 
2) A term with specific annotation examples, including a PMID reference and protein identifiers:
GO:0097345 mitochondrial outer membrane permeabilization
(http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0097345)
 
3) A term with annotation guidance on the dangers of mistaking an assay readout for a true process:
GO:0006309 apoptotic DNA fragmentation
(http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0006309)
</pre>
 
* Apoptosis annotation guide is available on the wiki - http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual
* Ruth has started a table cataloging some information. She will circulate it when ready.
* We can now store annotation example in the ontology itself. When you are requesting a term, please try to include an example

Latest revision as of 16:30, 9 April 2014

Agenda

Present:
SGD: Rama, Diane, Paul
MGI:David, Li
EBI- Paola, Rachael, Pablo
WB- Kimberley
Dicty- Petra, Pascale
Berkeley: Moni
UCL: Ruth, Paul and Ana


Review of apoptosis related genes (Pascale)

http://wiki.geneontology.org/index.php/PAINT_-_Apoptosis

QA checks in UniProt and Jenkins (Rachael)

There are checks that are not included in Jenkins but that UniProt-GOA does have checks for.

Jenkins checks for obsolete relations and checks GO terms in annotation extensions, but does it check for appropriate use of relations, e.g. if an entity type is out of range? Does it check for orphan ISS?

If Jenkins can't incorporate these checks, are groups interested in UniProt sending each group an error log for their annotations?

For example, the PomBase Jenkins check is clean; http://build.berkeleybop.org/job/gaf-check-pombase/lastSuccessfulBuild/artifact/gaf-validation-report.txt

but the UniProt-GOA check brings up several errors in 'domain/range';

e.g.
[[GO:0005829] [happens_during(GO:0034605)] [Invalid domain for happens_during: GO:0005829]]
[[GO:1990188] [not_dependent_on(PomBase:SPCC736.11),occurs_at(SO:0001843)] [Invalid range for occurs_at: SO:0001843]]
[[GO:1990188] [not_dependent_on(PomBase:SPCC736.11),occurs_at(SO:0001843)] [Invalid range for occurs_at: SO:0001843]]

ACTION:

We will add rules to GO rule xml file

Coming soon

  • Feb 24th: David OS will talk about formalizing the representation of symbiotic relationships and annotations to describe them in the ontology
    • GO annotations include many that involve an interaction between two organisms. These include:

annotation to a cell component of the host of the organisms expressing the gene being annotated. annotation to a biological process involving a virus and and its host.

In these cases we have a mechanism for recording multiple taxon IDs for interacting organisms, but not the relationship between the two organisms , e.g one might be host to the other or vector for the other. We also don't have a way to record which of the two interacting organisms a cell component is located in or a biological process is occurring in.

My proposal aims to solve this problem, by allowing annotators to link taxon IDs using a relationship such as host_of or vector_for. Additionally you will be able to use annotation extension to record which of the two organisms an annotated CC is located in or a biological process occurs in.

Along with this extension to annotation, I plan to rearrange parts of the CC hierarchy - particularly those relating to host cell. My presentation will include details of these changes.

  • TBA: Sandra Orchard will talk about the IntAct Complex portal

Discussion

Apoptosis

  • lot of annotations moved upstream. Assay read out and the process involved are different. Paola has added comments to terms where applicable to clarify.
1) A term with detailed annotation guidance and general annotation examples:
GO:0097527 necroptotic signaling pathway
(http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0097527)

2) A term with specific annotation examples, including a PMID reference and protein identifiers:
GO:0097345 mitochondrial outer membrane permeabilization
(http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0097345)

3) A term with annotation guidance on the dangers of mistaking an assay readout for a true process:
GO:0006309 apoptotic DNA fragmentation
(http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/GO:0006309)
  • Apoptosis annotation guide is available on the wiki - http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual
  • Ruth has started a table cataloging some information. She will circulate it when ready.
  • We can now store annotation example in the ontology itself. When you are requesting a term, please try to include an example