Difference between revisions of "Progress Reports"

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=April: Salt Lake City GOC Meeting=
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This page gathers links to all progress reports generated for the GO project, including monthly reports from each management group, reports prepared for GO Consortium meetings, and annual reports prepared for the NIH grant. The collection of publications, tutorials, etc. is also linked at the bottom of the page.
  
== SO Sequence Ontology==
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=Grant Progress Reports=
== Production Systems (Stanford)==
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*[https://drive.google.com/drive/folders/1Bv-7MIGpSzXxa7F6CkbhfKzoAcusydGs Grant Progress report 2019]
== Ontology Development==
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*[https://drive.google.com/drive/folders/1qoT_E4R_rrkEpDwjqtyfvqrgt66v5Xp9 Grant Progress report 2018]
===Metrics===
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*[[Grant_Progress_reports_2017]] / [https://drive.google.com/drive/folders/1gPwgQvRsJMEkahF55-bpm0WxJQ5Wfrqh Grant Progress Reports 2017 - Google drive]
====GO term statistics====
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*[[Grant_Progress_reports_2016]] / [https://drive.google.com/drive/folders/0B8kRPmmvPJU3SzNuZ0YzVVJEOWc Grant Progress Reports 2016 - Google drive]
'''October 1, 2007'''
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*[[Grant_Progress_Reports_2015]]
{| border="1" cellpadding="5" cellspacing="0"
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*[[Grant_Progress_Reports_2014]]
! !!Current!!Defined!!Obsolete!!Total
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*[[Grant_Progress_Reports_December_2013]]
|-
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*[[Grant_Progress_Reports_December_2012]]
|Function||7879||7492||556||8435
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*[[Grant_Progress_Reports_December_2010]]
|-
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*[[Grant_Progress_Reports_December_2009]]
|Process||13916||13757||458||14374
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*[[Grant_Progress_Reports_December_2008]]
|-
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*[[Grant_Progress_Reports_2007]]
|Component||2019||2019||114||2133
 
|-
 
|'''All'''||'''23814'''||'''24396'''||'''1128'''||'''24942'''
 
|}
 
  
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=Monthly Managers' Progress Reports=
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==User Advocacy & Annotation Outreach==
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*[[Annotation_Outreach_group_reports]]
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*[[Annotation_Advocacy_Roadmap]]
  
'''April 16, 2008'''
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==Ontology Development==
{| border="1" cellpadding="5" cellspacing="0"
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*[[Ontology_Development_reports|Ontology Development report list]]
! !!Current!!Defined!!Obsolete!!Total
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*[[2011_Timeline|Ontology Development Timeline]]
|-
 
|Function||8262||7909||566||8828
 
|-
 
|Process||14702||14564||470||15172
 
|-
 
|Component||2077||2077||117||2194
 
|-
 
|'''All'''||'''25041'''||'''25703'''||'''1153'''||'''26194'''
 
|}
 
  
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==Reference Genomes==
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*[[Reference_Genome_Progress_Reports]]
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*[[Reference_Genome_Timeline]]
  
====SourceForge statistics (Oct. 1 - April 17)====
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==Software & Utilities==
*items opened: 500
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*[[Software_and_Utilities#Reports|Software and Utilities group reports]]
*items closed: 476
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*[[OBO-Edit_Development_Monthly_Reports|OBO-Edit Development reports]]
====SourceForge reports (on SF site)====
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*[[SWUG_Timeline_2010-2011|Timeline2010-2011]]
*[https://sourceforge.net/tracker/reporting/index.php?atid=440764&what=aging&span=12&period=month&group_id=36855| "Aging Report" for past year]
 
*[https://sourceforge.net/tracker/reporting/index.php?atid=440764&what=resolution&span=12&period=month&group_id=36855| "Distribution by Resolution" for past year]
 
  
===Completed work===
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=GOC Meeting Progress Reports=
====''Regulates'' relationship====
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*[[Consortium_Meetings#Progress_Reports|Meeting progress report links on meetings page]]
Our most notable accomplishment since the [[GO 18th Consortium Meeting|Princeton meeting]] in September is that the '''regulates''' relationships have gone live. Chris, David and Tanya did an enormous amount of work, which is documented in the [[Regulation Main Page|regulation]] section of the wiki. A brief  [[Regulation metrics|summary of metrics]] is also available.
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**[[Meeting_Progress_Reports_November_2011]]
====Other completed work====
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**[[Meeting_Progress_Reports_May_2011]]
*The revamp of [[Sensu Main Page|Sensu]] terms is now complete. We described our approach of renaming terms and, where necessary, improving definitions or merging terms, at the September meeting.
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**[[Meeting_Progress_Reports_March_2010]]
*We reported on the [[Cardiovascular physiology/development]] and [[Muscle Development]] content meetings at the September meeting. Changes stemming from those meetings have gone live.
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**[[Meeting_Progress_Reports_September_2009|Meeting Progress Reports September 2009]]
*Smaller-scale efforts include:
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**[[Meeting_Progress_Reports_March_2009|Meeting Progress Reports March-April 2009]]
**A number of disjointness violations have been corrected.
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**[[Meeting_Progress_Reports_October_2008]] (collection of links to individual reports)
**[[Electron transport]] terms have been reorganized.
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**[[Meeting_Progress_Report_April_2008]] (one big report page)
**New enzyme-activity function terms and (many!) synonyms added, improving consistency with EC.
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*[[Consortium_Meetings#Progress_Report_Templates|Meeting progress report templates]]
**Process and component terms for plasma lipoprotein particles added.
 
**[[Sporulation Meeting Notes|Sporulation]] terms have been reorganized, and new terms added (connected with 'sensu' work).
 
**More [[PAMGO_2007|new terms]] have been added for PAMGO.
 
**PIR GO slim added.
 
===Work in progress===
 
*Two pilot projects to add [[Function-Process Links|links between the function and process ontologies]] are going on. Progress and future directions will be discussed during the meeting.
 
*A content meeting on [[Lung Development|lung development]] was held December 5-6. Progress will be briefly noted during the meeting.
 
*Jen has started gathering information and identifying experts to work on an overhaul of [[Signaling|signal transduction]] process terms.
 
====Collaboration with IMG====
 
Jane is working with Iain Anderson from IMG. The first set of IMG terms (about 1800) from April 2007 have been mapped and sent back, but since then another approx 1500 terms have been added to IMG and I am currently mapping these. The IMG pathways and parts also require mapping. <br>
 
  
I am collaborating with Antonio Jimeno from Dietrich Rebholz-Schuhmann's group (EBI) to create automatic mappings for these terms, which I then manually verify and return the data to him to improve the algorithms. We hope to eventually use this work to create a generic vocabulary mapping tool.
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=Publications, tutorials, talks, posters=
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*[[Publications, tutorials, talks, posters]]
  
== Reference Genome Project==
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[[Category:Reports]]
===Target genes===
 
- There are currently 394 genes in the Target gene list.
 
- Selection of genes: Since Nov 2007, we rotate the group selecting target genes.
 
- Curation priorities: Since Nov 2007, targets are not only disease genes anymore. We select 20 genes, 5 in each of 4 categories: (1) disease genes, (2) 'hot genes', (3) metabolic pathways, (4) uncharacterized.
 
 
 
===Annotation Progress===
 
{| border="1" cellpadding="5" cellspacing="0"
 
! Organism!!# genes looked at!!# genes with orthologs!!# genes curated
 
|-
 
|Arabidopsis ||372 ||131 (35%) ||129 (98%)
 
|-
 
|Caenorhabditis ||412 ||271 (66%) ||198 (73%)
 
|-
 
|Gallus ||99 ||82 (82%) ||none marked completed
 
|-
 
|Homo ||394 ||393 (99%) ||231 (59%)
 
|-
 
|Mus ||394 ||382 (97%) ||338 (88%)
 
|-
 
|Saccharomyces ||394 ||164 (41%) ||159 (95%)
 
|-
 
|Drosophila ||376 ||171 (45%) ||70 (41%)
 
|-
 
|Rattus ||394 ||347 (88%) ||250 (72%)
 
|-
 
|Danio ||374 ||283 (75%) ||264 (93%)
 
|-
 
|Dictyostelium ||331 ||148 (44%) ||53 (36%)
 
|-
 
|Schizosaccharomyces ||334 ||124 (37%) ||105 (85%)
 
|-
 
|Escherichia ||375 ||51 (13%)
 
|}
 
 
 
 
 
[[Image:2008-04-RefGenomeMetric-all_data.jpg]]
 
 
 
===Annotation Quality Control===
 
 
 
We are trying to address the issue of quality control of the annotations. Some of the concerns are:
 
* Omission of annotations
 
* Errors in annotations
 
* Absence of 'with' for ISS annotations or 'with' object not experimentally characterized
 
* Overannotation with ISS to process terms
 
* Problems in the ontology that can become evident when comparing annotations from different species
 
 
 
Methods to address this:
 
# There are some queries that can be done: for example, genes for which an ortholog has GO annotations and that is either lacking annotations or annotated to ND
 
# (Val Wood): Looking for co-occurences of annotations as a high-level way to check for errors
 
# Manual verification of ortho sets (Source forge tracker: http://sourceforge.net/tracker/?group_id=36855&atid=1040173
 
 
 
===Software development===
 
Currently the targets genes and annotation status are captured using Google spreadsheets (Target genes and links to every group's annotation status page can be found at http://spreadsheets.google.com/ccc?key=pwOksMOra5uq4vIYjPgefPw
 
 
 
# Ortho set curation status: Siddhartha Basu, Chris Mungall, Seth Carbon and Mary Dolan are working on a database and a tool where target genes (ortho sets) and their curation status will be maintained.
 
# Graphical displays (Mary Dolan): several improvements
 
# Integration of ref genomes genes into AmiGO
 
 
 
===Generating Ortholog sets===
 
P-POD: Kara Dolinski (Princeton) : Procedure:
 
# Obtain FASTA files from each group from gp2protein files
 
# all vs all BLAST
 
# Ortho MCL
 
# ClustalW
 
# PHYLIP
 
* Notung
 
* Output will be rooted trees reconciled with species tress, graphic image of tree
 
* We are on the Notung step right now and are adding data as they are generated.  Currently, OrthoMCL families can be queried by gene name, though you just get back a list of members right now.  Data are being made available as soon as we have them:
 
 
 
Web interface:
 
[http://ppod.princeton.edu/cgi-bin/ppod.cgi http://ppod.princeton.edu/cgi-bin/ppod.cgi]
 
FTP site:
 
[ftp://gen-ftp.princeton.edu/ppod/go_ref_genome/  ftp://gen-ftp.princeton.edu/ppod/go_ref_genome/ ]
 
 
 
===Communication===
 
The reference genome group holds a monthly phone conference.  Minutes can be found at
 
[[Conference_Calls]]
 
 
 
== Software and Utilities==
 
== User Advocacy==
 
===GO helpdesk===
 
Continues to be run efficiently. The email system was recently moved to Mailman. [will enter stats when I have them]
 
===GO newsletter===
 
Two editions since the last meeting. We have applied for an ISSN for the newsletter.
 
=== Web-presence Working Group (formerly AmiGO WG)===
 
AmiGO 1.5 was released earlier this month with many new features including a GO slimmer tool, a term enrichment tool and SQL search interface. We are now beginning to set priorities for the next release.
 
<br>
 
The advocacy group has not been involved with AmiGO development recently, but in the future we have decided that the advocacy group will be involved in setting priorities, from a biologist's perspective, at the beginning of a release and working with the software group to come up with a release plan. The software group will develop the release independently, with advocacy only getting involved again when testing in the run-up to the release is required.
 
 
 
==Outreach==
 
 
 
Outreach group activity reduced to supporting groups who approach GO directly. We are not currently actively seeking out new annotation groups.
 
 
 
===Major Developments:===
 
 
 
* Group at CRIBI (Italy) committed to carrying out grape annotation.
 
* Plant Physiology journal have agreed to accept annotations from submitting authors. (TAIR collaboration)<br>
 
[[http://wiki.geneontology.org/index.php/Image:PlantPhysiol.png online submission tool]]<br>
 
* TAIR outreach at PAG 2008. Discussion of community annotation with TAIR, SGN (SOL Genomics Network) and WormBase.
 
* Sol Genomics Network database annotation file has been submitted.
 
* Reactome have created annotation files according to the plans laid down in Princeton, and are ready to commit when they have cvs access. (Emily Dimmer and Esther Schmidt)
 
* ISAFG Conference - Fiona McCarthy reports continuing interest in GO.
 
* Muscle Annotation wiki (Erika Feltrin and Alex Diehl)
 

Latest revision as of 03:26, 22 November 2019

This page gathers links to all progress reports generated for the GO project, including monthly reports from each management group, reports prepared for GO Consortium meetings, and annual reports prepared for the NIH grant. The collection of publications, tutorials, etc. is also linked at the bottom of the page.

Grant Progress Reports

Monthly Managers' Progress Reports

User Advocacy & Annotation Outreach

Ontology Development

Reference Genomes

Software & Utilities

GOC Meeting Progress Reports

Publications, tutorials, talks, posters