Annotation Conf. Call 2020-01-21: Difference between revisions
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(Created page with "= Agenda and Minutes = *Present: == Pipeline == *gp2protein files **plan is to [https://github.com/geneontology/go-site/issues/400 retire these from GOC], but want to double...") |
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= Agenda and Minutes = | = Agenda and Minutes = | ||
*Present: | *Present: Chris, David, Dmitry, Edith, Harold, Karen, Kimberly, Laurent-Philippe, Li, Michele, Patrick, Pascale, Penelope, Petra, Rob, Sabrina, Stan, Suzi, Tremayne, Val | ||
== Pipeline == | == Pipeline == | ||
*gp2protein files | *gp2protein, gp2rna, gp_unlocalized files | ||
**plan is to [https://github.com/geneontology/go-site/issues/400 retire these from GOC], but want to double-check if there is any use for these files that would require GOC to keep them | **plan is to [https://github.com/geneontology/go-site/issues/400 retire these from GOC], but want to double-check if there is any use for these files that would require GOC to keep them | ||
*Announcement sent to go-friends, 2020-01-16 | *Announcement sent to go-friends, 2020-01-16 | ||
**https://github.com/geneontology/go-site/issues/1324 | **https://github.com/geneontology/go-site/issues/1324 | ||
**https://github.com/geneontology/go-announcements/issues/93 | **https://github.com/geneontology/go-announcements/issues/93 | ||
*Summary of ticket: | |||
**the GOC pipeline is not using gp2protein files for any data processing | |||
**gpi files | |||
***produced as complementary file for gpad | |||
***produced to populate annotatable entity ontology for Noctua | |||
*Possible future work | |||
**a gene/gene product identifier mapping file, with clear semantics, would be of use to the broader scientific community | |||
**exact file format, who should produce this file, how should it be distributed might all be topics for discussion | |||
***GO's gpi file format | |||
***Alliance bgi.json | |||
***UniProtKB also produces an [ftp://ftp.ebi.ac.uk/pub/databases/reference_proteomes/QfO/Eukaryota/ idmapping file] as part of the Quest for Orthologs work | |||
***MODs may also have id mapping files (e.g. WB ftp) | |||
**form a working group of representatives from the Alliance and other databases/projects to develop a common standard here? | |||
**breakout session at ISB in Bar Harbor? | |||
***GO's gpi file format might be a good place to start | |||
***UniProtKB also produces an [ftp://ftp.ebi.ac.uk/pub/databases/reference_proteomes/QfO/Eukaryota/ idmapping file] as part of the Quest for Orthologs work | |||
'''*ACTION: Chris, Kimberly, Stacia to follow-up offline to see what concrete steps could be taken to move discussion forward on a more broadly used id mapping file | |||
== Noctua Form 2.0 == | == Noctua Form 2.0 == | ||
* | *Software updates made to ensure correct environment of all components | ||
*Additional updates: | |||
**Entity identifiers now displayed along with labels (particularly helpful when annotating gene product isoforms) | |||
**Causal relations decision tree (available via Connect on the Noctua form table) | |||
*Available (SOON!) from [http://noctua.geneontology.org/ Noctua landing page] and workbenches menu on graph editor (NOW) | *Available (SOON!) from [http://noctua.geneontology.org/ Noctua landing page] and workbenches menu on graph editor (NOW) | ||
*[http://wiki.geneontology.org/index.php/Noctua Noctua Manual] | *[http://wiki.geneontology.org/index.php/Noctua Noctua Manual] | ||
Line 16: | Line 37: | ||
*ACTION: curators should try out the new form, give us feedback; we will continue to update and organize the documentation to try to help with workflow | *ACTION: curators should try out the new form, give us feedback; we will continue to update and organize the documentation to try to help with workflow | ||
== | '''*ACTION: New software updates on Noctua development site will be rolled out to production; Kimberly will email when new Noctua form is on production. | ||
* | |||
* | == Annotation Relations == | ||
** | *Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible | ||
** | *Review retired relations: | ||
*** | **'has direct input' -> 'has input' for MF | ||
*ACTION: | **'occurs at' -> 'occurs in' for MF | ||
**annotation tools need to updated | |||
'''*ACTION: Groups that have these relations in their annotation tools, should remove them. | |||
'''*ACTION: Commented on [https://github.com/oborel/obo-relations/issues/187 existing ticket in RO tracker] to obsolete 'has direct input'. | |||
[[Category:Annotation Working Group]] | [[Category:Annotation Working Group]] |
Latest revision as of 12:57, 21 January 2020
Agenda and Minutes
- Present: Chris, David, Dmitry, Edith, Harold, Karen, Kimberly, Laurent-Philippe, Li, Michele, Patrick, Pascale, Penelope, Petra, Rob, Sabrina, Stan, Suzi, Tremayne, Val
Pipeline
- gp2protein, gp2rna, gp_unlocalized files
- plan is to retire these from GOC, but want to double-check if there is any use for these files that would require GOC to keep them
- Announcement sent to go-friends, 2020-01-16
- Summary of ticket:
- the GOC pipeline is not using gp2protein files for any data processing
- gpi files
- produced as complementary file for gpad
- produced to populate annotatable entity ontology for Noctua
- Possible future work
- a gene/gene product identifier mapping file, with clear semantics, would be of use to the broader scientific community
- exact file format, who should produce this file, how should it be distributed might all be topics for discussion
- GO's gpi file format
- Alliance bgi.json
- UniProtKB also produces an idmapping file as part of the Quest for Orthologs work
- MODs may also have id mapping files (e.g. WB ftp)
- form a working group of representatives from the Alliance and other databases/projects to develop a common standard here?
- breakout session at ISB in Bar Harbor?
- GO's gpi file format might be a good place to start
- UniProtKB also produces an idmapping file as part of the Quest for Orthologs work
*ACTION: Chris, Kimberly, Stacia to follow-up offline to see what concrete steps could be taken to move discussion forward on a more broadly used id mapping file
Noctua Form 2.0
- Software updates made to ensure correct environment of all components
- Additional updates:
- Entity identifiers now displayed along with labels (particularly helpful when annotating gene product isoforms)
- Causal relations decision tree (available via Connect on the Noctua form table)
- Available (SOON!) from Noctua landing page and workbenches menu on graph editor (NOW)
- Noctua Manual
- User Guide - Google doc from Berkeley meeting, will be retired
- ACTION: curators should try out the new form, give us feedback; we will continue to update and organize the documentation to try to help with workflow
*ACTION: New software updates on Noctua development site will be rolled out to production; Kimberly will email when new Noctua form is on production.
Annotation Relations
- Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
- Review retired relations:
- 'has direct input' -> 'has input' for MF
- 'occurs at' -> 'occurs in' for MF
- annotation tools need to updated
*ACTION: Groups that have these relations in their annotation tools, should remove them.
*ACTION: Commented on existing ticket in RO tracker to obsolete 'has direct input'.