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Ontology Development Report - February 2010
Ontology Development Report - March 2010


===I. Ontology Development===
===I. Ontology Development===
*SourceForge
====Tracker====
**Items opened:  
*Items opened: 127
**Items closed:  
*Items closed: 128
**Items still open:  
*Items still open: 239
***assigned:  
**assigned: 150
***unassigned:  
**unassigned: 89


*Completed content items
====Completed content items====
**[[Signaling]]: The signaling branch has been committed and the project is being carried forward by Becky Foulger. [Jen]
*[[Kidney_Development|Kidney development]] - the metanephros terms have been finished [Midori]
**[[Taxon_Main_Page|Taxon triggers]]: The files are now in their permanent location in cvs and most of the problematic annotations and mappings have been fixed. The ontology issues are being worked on. The project will be taken over by Jane and a new member of staff at GOA. [Jen]
*Various SourceForge items
**Various SourceForge items


*Content items in progress
====Content items in progress====
**Further discussion on aligning with ChEBI for [[XP:biological_process_xp_chebi|cross-products]] (Midori, Chris, Jane, David, ChEBI curators); David and Tanya visiting Cambridge in March to standardize GO implicit chemical ontology
*[[Signaling]]- working through the existing signaling terms to make them more consistent and fill in any gaps. Intracellular signaling terms, and regulation of signaling is on the agenda for the conference call next week. [Becky]
**[[Kidney_Development|Kidney development]] meeting follow-up work in progress [Midori & David]
*[[Chemical_terms_in_GO]] - continuing to edit the GOCHE ontology (chemicals in GO) [David, Tanya, Jane & Harold]
**Working on two new sets of PAMGO terms, see [https://sourceforge.net/tracker/?func=detail&aid=2949110&group_id=36855&atid=440764] and [http://listserv.vbi.vt.edu/archives/pamgo-discussion/2010-01/threads.html] [Jane]
*Further work in collaboration with with NIF (Neuroscience Information Framework) [Jane & Chris]
**Added a new set of terms for axon-related cellular components in collaboration with NIF (Neuroscience Information Framework) [Jane & Chris]
*Review of bp x bp internal cross-product set, see [[CJM_EBI_Visit_June_2009#Status_overview_and_release_plan|plan to add internal cross-products]]. [David & Tanya]
**Review of internal cross-product sets such as BP-xp-self and CC-xp-self continues; see [[CJM_EBI_Visit_June_2009#Status_overview_and_release_plan|plan to add internal cross-products]]. (Jen, Jane, Midori, Chris, David, Tanya)
*Adding lots of [[Transmembrane_transporters | transmembrane transport terms]] for Val's goslim mappings. [Becky]
**Continuing to add [[Function-Process_Links|function-process]] part-of links in gene_ontology_write.obo and gene_ontology_ext.obo (David, Tanya)
*Standardizing the GO terms that contain the word 'during'. [David & Tanya]
**Work continues on overhauling [[Virus_terms|terms related to viruses]] (Jane)
*Quality control continues as usual - reports generated by Chris (cronjobs)
**Quality control continues as usual - reports generated by Chris (cronjobs)
**Reasoner-based implied links for new regulation terms - also see above (David, Tanya)
***Reasoner-based implied links for new regulation terms - also see above (David, Tanya)
**Multiple part_of parents (several GO curators, especially Tanya & David)
***Multiple part_of parents (several GO curators, especially Tanya & David)
**Abduced links [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/regulates_xp_live/go_reglive_withPosNeg_withPF-abduced-links.txt]](David, Tanya)
***Abduced links [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/regulates_xp_live/go_reglive_withPosNeg_withPF-abduced-links.txt]](David, Tanya)
**Problematic regulates terms [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/regulates_xp_live/report-filtered.txt]](David, Tanya)
***Problematic regulates terms [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/regulates_xp_live/report-filtered.txt]](David, Tanya)


*Publications
====Publications====
**Manuscript on [[Taxon_Main_Page|Taxon triggers]] almost ready for submission to BMC Bioinformatics (Jen, Chris)
*Case studies for publication on "revisability" of GO, proposed and coordinated by [http://huss.exeter.ac.uk/sociology/staff/leonelli/index.php Sabina Leonelli] - in progress (Midori, Jane, Alex, Karen C)
**New PAMGO paper "Unifying themes in microbial associations with animal and plant hosts described using the Gene Ontology" ready for submission to Microbiology and Molecular Biology Reviews
**Case studies for publication on "revisability" of GO, proposed and coordinated by [http://huss.exeter.ac.uk/sociology/staff/leonelli/index.php Sabina Leonelli] - in progress (Midori, Jane, Alex, Karen C)
**Continued from November & December:
***Resuming work on manuscript on regulates relations (Jane, Midori, David, Chris, Tanya, maybe other annotators)


*Anything else
====Anything else====
**Jen going on maternity leave from the 1st March 2010 to the 28th February 2011.
*Applications now closed for EBI GO curator position
**Becky Foulger from UniProt is joining us until the May 14th 2010 
*GO bibliography has 3164 entries
**GO bibliography has 3164 entries


[[Ontology_Development_reports|Back to list]]
[[Ontology_Development_reports|Back to list]]


[[Category:Reports]]
[[Category:Reports]]
[[Category:Ontology]]

Latest revision as of 06:03, 14 April 2010

Ontology Development Report - March 2010

I. Ontology Development

Tracker

  • Items opened: 127
  • Items closed: 128
  • Items still open: 239
    • assigned: 150
    • unassigned: 89

Completed content items

  • Kidney development - the metanephros terms have been finished [Midori]
  • Various SourceForge items

Content items in progress

  • Signaling- working through the existing signaling terms to make them more consistent and fill in any gaps. Intracellular signaling terms, and regulation of signaling is on the agenda for the conference call next week. [Becky]
  • Chemical_terms_in_GO - continuing to edit the GOCHE ontology (chemicals in GO) [David, Tanya, Jane & Harold]
  • Further work in collaboration with with NIF (Neuroscience Information Framework) [Jane & Chris]
  • Review of bp x bp internal cross-product set, see plan to add internal cross-products. [David & Tanya]
  • Adding lots of transmembrane transport terms for Val's goslim mappings. [Becky]
  • Standardizing the GO terms that contain the word 'during'. [David & Tanya]
  • Quality control continues as usual - reports generated by Chris (cronjobs)
    • Reasoner-based implied links for new regulation terms - also see above (David, Tanya)
    • Multiple part_of parents (several GO curators, especially Tanya & David)
    • Abduced links [[1]](David, Tanya)
    • Problematic regulates terms [[2]](David, Tanya)

Publications

  • Case studies for publication on "revisability" of GO, proposed and coordinated by Sabina Leonelli - in progress (Midori, Jane, Alex, Karen C)

Anything else

  • Applications now closed for EBI GO curator position
  • GO bibliography has 3164 entries

Back to list