GO Internal

QC/QA Group

GO wiki (new pages) - Mon, 03/19/2018 - 10:16

Pascale:

=Objective=
The QC/QA group aims to identify any issues that may negatively impact the quality of the products developed by the GOC. The group was formed in October 2017.

= Group Leaders =
Pascale Gaudet (GOC), Kimberly Van Auken (WB), Sylvain Poux (Swiss-Prot), Val Wood (PomBase)


= Communication =
The groups meets on an irregular basis.

==Conference call minutes and agendas==
[[QCQA call March 20, 2018]]

[[Category:Quality Control]] Pascale
Categories: GO Internal

Ontology meeting 2018-03-19

GO wiki (new pages) - Mon, 03/19/2018 - 05:35

David: /* Editors Discussion */

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =


==GH project link==
https://github.com/geneontology/go-ontology/projects/1


== Editors Discussion ==
* Request from Birgit: Can we send an email to go-consortium or go-friends to announce that protein complex has been merged?
https://github.com/geneontology/go-ontology/issues/15421

* Should we make it a standard SOP that when there is an ontology structure issue that is the result of an imported ontology, we ask the requester to contact the source ontology directly?

= Minutes =
*On call:


[[Category: Ontology]]
[[Category: Meetings]] Pascale
Categories: GO Internal

Transcription 2018 - 2018-03-15 meeting: review BP terms

GO wiki (new pages) - Thu, 03/15/2018 - 01:21

Pascale:

==Objective==
In the BP aspect of the ontology, transcription is classified in two axes:
* by the promoter/polymerase responsible for the transcription
* by the transcript type (mRNA, etc).
However both the ontology and the annotations are inconsistent:
* Not all transcript types have a process
* Not all transcript types have a regulation of transcription

There is a proposal here as to how to merge terms so that the main axis of classification is the biological output (ie, the transcript type); and secondary, the polymerase, for cases for which more than one polymerase is known to transcribe a specific product
https://docs.google.com/spreadsheets/d/1UMwBT4pAJBqUHXYTG2K1bL60ok6QkWPJ3yVFX29nGRQ/edit#gid=0

The first task for the groups is to review a sample of the existing annotations to see if that proposal could be implemented and support accurate annotation, as well as to look at the latest techniques in the field to also ensure that the newer literature is covered in the new structure of the ontology we will propose.







==Review BP: miRNA transcription==
Ruth


Two key findings

In summary there seems to be growing evidence for pri-microRNA transcription by RNA pol III as well as by Pol II

PMID: 21607569 (2011) Introduction statement: Most of the miRNA genes, which are located predominantly in introns of protein coding genes and intergenic regions, are transcribed by RNA polymerase II (Pol II) [11, 12], and some are transcribed by RNA polymerase III (Pol III) [13] (Fig. 1).
Ref 13 from above is: PMID: 17099701 RNA polymerase III transcribes human microRNAs.https://www.ncbi.nlm.nih.gov/pubmed/?term=17099701
In PubMed there are over 400 papers listed with the search RNA polymerase III microRNAs.
https://www.ncbi.nlm.nih.gov/pubmed/29136251 (2018) authors suggests they have the first comprehensive evidence for RNA polymerase III mediated transcription of microRNAs (the miRs looked at here are all associated with Alu repeats which are apparently transcribed by Pol III).

The other task I was supposed to do was looking for evidence that papers are confirming Pol II is responsible for transcription. I decided just to check the papers that have already been annotated rather than looking at papers not yet annotated.
Looking at a selection of papers annotated to the pri-miRNA transcription and child terms, it seems that in the majority of cases there is no evidence confirming the RNA polymerase involved, and no mention of RNA polymerase II (7 no mention; 1 evidence for RNA pol II; 2 mention of RNA pol II but no evidence).
One paper I have looked at so far mentions RNA Pol II: PMID:18548003 (2008), but this paper demonstrates RNA polymerase II not involved with this statement in results: Likewise, BMP4-mediated induction of both pre-miR-21 and mature miR-21 was resistant to inhibition of RNA polymerase II by α-amanitin, whereas induction of the BMP4 transcriptional target gene ID1 (ref. 30) was abolished.
This data could imply just that there is a ton of pri-miRNA available and therefore it is just the processing that affects whether pre-miR-21 and mature miR-21 are induced. Ie no further transcription is required. But based on the statements above it is possible that this result was due to RNA pol III transcribing this pri-miRNA. Although the paper does additionally provide evidence that SMADs are involved in regulating the processing of these RNAs.
https://www.ncbi.nlm.nih.gov/pubmed/?term=21441434%5Buid%5D Arabidopsis paper (2011); anti-Pol II ChIP used to confirm miRNA transcription regulated by increasing Pol II occupancy at miRNA TSS.
I have only looked at 10 of the 38 papers that have been annotated to pri-miRNA transcription and child terms

I would there suggest that the term GO:0061614 pri-miRNA transcription by RNA polymerase II needs a more general parent pri-miRNA transcription, and a more specific child term pri-miRNA transcription by RNA polymerase III.
Or that we just have the BP term: pri-miRNA transcription



==RNA polymerase studied with ChIP==
Astrid

I did a quick search for papers on RNA polymerase studied with ChIP and see indeed there are many.
I have now in depth analysis of these papers, but below just one example of a review paper (PMID: 21540878) summarizing what can be leared about RNA pol III transcription from ChIP based analyses




Nat Rev Genet. 2011 May 4;12(7):459-63. doi: 10.1038/nrg3001.
Transcription by RNA polymerase III: more complex than we thought.
White RJ.
RNA polymerase (Pol) III is highly specialized for the production of short non-coding RNAs. Once considered to be under relatively simple controls, recent studies using chromatin immunoprecipitation followed by sequencing (ChIP-seq) have revealed unexpected levels of complexity for Pol III regulation, including substantial cell-type selectivity and intriguing overlap with Pol II transcription. Here I describe these novel insights and consider their implications and the questions that remain.


==Review BP: mRNA transcription and RNA poly II transcription==
Pascale

[[Category:Transcription]] [[Category:Ontology]] Pascale
Categories: GO Internal

Transcription 2018

GO wiki (new pages) - Thu, 03/15/2018 - 01:19

Pascale: Created page with "Transcription 2018 - 2018-03-15 meeting: review BP terms Category:Transcription Category:Ontology"

[[Transcription 2018 - 2018-03-15 meeting: review BP terms]]






[[Category:Transcription]] [[Category:Ontology]] Pascale
Categories: GO Internal

Cam

GO wiki (new pages) - Wed, 03/14/2018 - 16:38

Lpalbou: Created page with "Category:CAM This page is not yet available, please come back later To access documentations, <span class="plainlinks">[http://wiki.geneontology.org/index.php/cam/docs/..."

[[Category:CAM]]

This page is not yet available, please come back later

To access documentations, <span class="plainlinks">[http://wiki.geneontology.org/index.php/cam/docs/ click here]</span> Lpalbou
Categories: GO Internal

Cam/docs/development

GO wiki (new pages) - Wed, 03/14/2018 - 15:58

Lpalbou:

[[Category:CAM]]

= Preamble =
GO-CAM models are based on the semantic annotation and combination of biological facts. Each fact or statement corresponds to a standard GO Annotation, that is a Gene associated to a GO-Term. To read more about standard GO annotations, <span class="plainlinks">[http://geneontology.org/page/go-annotations click here]</span>.

GO-CAM relies on the <span class="plainlinks">[http://geneontology.org/page/ontology-documentation Gene Ontology]</span> to define a controlled set of vocabulary and enable curators to create structured biological facts, also called annotations. GO-CAM combines those single biological facts to describe and define larger biological processes. Each biological fact can be written as.a triplet <subject - predicate - object> and a model, as a collection of triplets, can be stored in TTL file.

The curators use the platform <span class="plainlinks">[http://noctua.geneontology.org Noctua]</span> to create these GO-CAM models. Noctua is the front-end, currently written with <span class="plainlinks">[https://github.com/janl/mustache.js/ mustache]</span> and <span class="plainlinks">[https://github.com/kltm/pup-tent pup-tent], and allows for the creation of workbenches (end-user UI to access and manipulate the models in different ways)

= General Architecture =
* Front-end: Noctua (mustache / pup-tent
* Middleware: Barista (NodeJS)
* Back-end: Minerva (Jetty)

Minerva uses Blazegraph as a triple store to save each model (TTL file). The collection of these models in blazegraph is called a journal. To know more about blazegraph, <span class="plainlinks">[https://wiki.blazegraph.com/wiki/index.php/Quick_Start click here]</span>

= First Steps =
* <span class="plainlinks">[https://github.com/geneontology/noctua#the-noctua-editor--barista--minerva-stack Noctua Full Stack]</span>
* <span class="plainlinks">[https://github.com/geneontology/minerva/blob/master/INSTRUCTIONS.md Minerva Setup]</span>
* <span class="plainlinks">[https://github.com/geneontology/noctua/issues/270 Barista Credentials]</span>
* <span class="plainlinks">[https://github.com/geneontology/minerva/blob/master/specs/owl-model.md GO-CAM specification]</span>
* <span class="plainlinks">[https://github.com/berkeleybop/bbop-manager-minerva/wiki/MinervaRequestAPI Minerva Request API]</span>
* <span class="plainlinks">[https://github.com/geneontology/noctua-repl Noctua REPL]</span>

= Additional Resources =
* <span class="plainlinks">[https://docs.google.com/document/d/1w3mkF1RQIzwROOCMTkqjYaOn8ZbdsW52t-xA4DKt0vg/edit#heading=h.du3v9zif59jp Noctua Full Stack Description]</span>
* <span class="plainlinks">[https://docs.google.com/document/d/1ScazN8xL8iMpiPvSO3zBZ9AVsOs8LULvb9aMpwHsKkk/edit Noctua Workbench Description]

<br>
<br> Lpalbou
Categories: GO Internal

Cam/docs/research

GO wiki (new pages) - Wed, 03/14/2018 - 15:58

Lpalbou:

[[Category:CAM]]

= Preamble =
GO-CAM models are based on the semantic annotation and combination of biological facts. Each fact or statement corresponds to a standard GO Annotation, that is a Gene associated to a GO-Term. To read more about standard GO annotations, <span class="plainlinks">[http://geneontology.org/page/go-annotations click here]</span>.

GO-CAM relies on the <span class="plainlinks">[http://geneontology.org/page/ontology-documentation Gene Ontology]</span> to define a controlled set of vocabulary and enable curators to create structured biological facts, also called annotations. GO-CAM combines those single biological facts to describe and define larger biological processes. Each biological fact can be written as.a triplet <subject - predicate - object> and a model, as a collection of triplets, can be stored in TTL file.

The curators use the platform <span class="plainlinks">[http://noctua.geneontology.org Noctua]</span> to create these GO-CAM models. Noctua is the front-end, currently written with <span class="plainlinks">[https://github.com/janl/mustache.js/ mustache]</span> and <span class="plainlinks">[https://github.com/kltm/pup-tent pup-tent], and allows for the creation of workbenches (end-user UI to access and manipulate the models in different ways)

= First Steps =
This documentation is not yet available, please come back later

= Additional Resources =

<br>
<br> Lpalbou
Categories: GO Internal

Cam/docs/curation

GO wiki (new pages) - Wed, 03/14/2018 - 15:53

Lpalbou:

[[Category:CAM]]

= Preamble =
GO-CAM models are based on the semantic annotation and combination of biological facts. Each fact or statement corresponds to a standard GO Annotation, that is a Gene associated to a GO-Term. To read more about standard GO annotations, <span class="plainlinks">[http://geneontology.org/page/go-annotations click here]</span>.

GO-CAM relies on the <span class="plainlinks">[http://geneontology.org/page/ontology-documentation Gene Ontology]</span> to define a controlled set of vocabulary and enable curators to create structured biological facts, also called annotations. GO-CAM combines those single biological facts to describe and define larger biological processes. Each biological fact can be written as.a triplet <subject - predicate - object> and a model, as a collection of triplets, can be stored in TTL file.

The curators use the platform <span class="plainlinks">[http://noctua.geneontology.org Noctua]</span> to create these GO-CAM models. Noctua is the front-end, currently written with <span class="plainlinks">[https://github.com/janl/mustache.js/ mustache]</span> and <span class="plainlinks">[https://github.com/kltm/pup-tent pup-tent], and allows for the creation of workbenches (end-user UI to access and manipulate the models in different ways)

= First Steps =
Curators should start with this <span class="plainlinks">[http://noctua.geneontology.org/doc/quick-start-guide Quick Start Guide]</span>

To dive deeper into the creation and curation of GO-CAM Models, curators are encouraged to follow this more <span class="plain links">[http://wiki.geneontology.org/index.php/Noctua Complete Guide]</span>.

= Additional Resources =
* <span class="plainlinks">[https://docs.google.com/document/d/1hmYNEP7lWFwWGJbDOHfsfDvT77yBNRH4IW1TAPyhdqg/edit# Additional Guide 1]</span>
* <span class="plainlinks">[https://docs.google.com/document/d/18ihslb7prB6CWtu2yjF-pMHZBTY1-AdXJAu-ZyuyXS4/edit# Additional Guide 2]</span>

<br>
<br> Lpalbou
Categories: GO Internal

Cam/docs/

GO wiki (new pages) - Wed, 03/14/2018 - 15:40

Lpalbou: Created page with "Category:CAM = Documentations ="

[[Category:CAM]]

= Documentations = Lpalbou
Categories: GO Internal

Cam/

GO wiki (new pages) - Wed, 03/14/2018 - 15:39

Lpalbou: Created page with "Category:CAM = Causal Activity Models ="

[[Category:CAM]]

= Causal Activity Models = Lpalbou
Categories: GO Internal

Docs Development

GO wiki (new pages) - Wed, 03/14/2018 - 15:35

Sjcarbon: Created page with "TBD Category:Documentation"

TBD

[[Category:Documentation]] Sjcarbon
Categories: GO Internal

Docs Curation

GO wiki (new pages) - Wed, 03/14/2018 - 15:34

Sjcarbon: Created page with "TBD Category:Documentation"

TBD

[[Category:Documentation]] Sjcarbon
Categories: GO Internal

Docs Research

GO wiki (new pages) - Wed, 03/14/2018 - 15:34

Sjcarbon: Created page with "TBD Category:Documentation"

TBD

[[Category:Documentation]] Sjcarbon
Categories: GO Internal

Enables

GO wiki (new pages) - Tue, 03/13/2018 - 16:37

Cjm: Created page with "== Overview == === Definition === === Child Terms === == Examples of Usage == == Quality Control Checks == == Relations Ontology == [http://www.ontobee.org/ontology/RO?iri=..."

== Overview ==
=== Definition ===
=== Child Terms ===

== Examples of Usage ==

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002327 enables]

== Review Status ==

Last reviewed: March 13, 2018

[[Category: Annotation]]
[[Category: Relations]]
[[Category: Gene Product to Term Relations]] Cjm
Categories: GO Internal

Contibutes to

GO wiki (new pages) - Tue, 03/13/2018 - 16:33

Cjm: /* Relations Ontology */

== Overview ==
=== Definition ===
=== Child Terms ===

== Examples of Usage ==

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes to]

== Review Status ==

Last reviewed: March 9, 2018

[http://wiki.geneontology.org/index.php/Biological_Process Back to: Biological Process]

[[Category: Annotation]]
[[Category: Relations]]
[[Category: Gene Product to Term Relations]] Cjm
Categories: GO Internal

Manager Call 2018-03-15

GO wiki (new pages) - Tue, 03/13/2018 - 10:32

Vanaukenk: /* RCA Evidence Code */

[[Category:GO Managers Meetings]]

= Call in info=
https://stanford.zoom.us/j/754529609

= Agenda =
== NYC Meeting Agenda ==
*Need to remind people to register & book rooms
*Start working on the agenda in more detail
**https://github.com/geneontology/go-ontology/milestone/5
**https://github.com/geneontology/go-annotation/milestone/2
*SAB agenda, plans

== Working Groups/Projects ==
=== Expanded Set of Relations ===
*Implementation requirements to meet our May goal of at least having acts_upstream_of_or_within
**Guidelines/examples for use
***acts upstream of: sperm motility, lipidation of ras, glycine transport -> heme biosynthesis
***regulation: glycolysis, signaling
***involved in: F-P links
***make use of other F-P co-annotation
***other ontology relations could be used to devise rules
***PAINT annotations
**Have a mechanism for groups to propose new rules
**Review annotations to process and regulation of process
***Can Mary D. generate lists for all groups, put on a webpage for review?
**Other software support needed for this?
=== Protein Complexes ===
=== HTP Codes ===
==== RCA Evidence Code ====
*Need to work with several groups to review their annotations:
**Gramene (35815 annotations)
**As an example, 2929 RCA Molecular Function annotations
***Date: 20060831
***Reference: [http://archive.gramene.org/db/literature/pub_search?ref_id=8030 GR_REF:8030]
***Manual review of mappings; can we suggest [http://wiki.geneontology.org/index.php/Inferred_from_Sequence_Model_(ISM) ISM]?
**GeneDB
**EcoCyc
**AgBase
**AspGD
**PAMGO_MGG

=== Documentation ===
=== QA/QC ===
=== Working Group Meetings ===
*Quarterly?
**Rotate between ontology and annotation (small, focused groups)
**Test virtual meetings, but still focused on the task

== Noctua ==
=== 1.0 Rollout ===
* Merge Tremayne's fork with Noctua-dev for further testing
* Some outstanding issues on SAE
* Single source file for MODs to consume
=== Reactome Imports ===
*David, Kimberly have looked at some imports/translations
*Ben's work looks to be potentially very useful and promising for seeding templates, models
*Will probably require significant manual input, refinement, testing
=== End User Tools ===
*What plans do we have for implementing consumption and display of GO-CAM models?
*How does the AGR GO working group fit into this task?
*https://github.com/geneontology/noctua/issues/519

== GO Helpdesk ==



= Minutes =
*On call: Vanaukenk
Categories: GO Internal

Annotation Relations

GO wiki (new pages) - Tue, 03/13/2018 - 06:59

Vanaukenk:

[[acts upstream of or within]]

[[acts upstream of or within, positive effect]]

[[acts upstream of or within, negative effect]]

[[acts upstream of, positive effect]]

[[acts upstream of, negative effect]]

[[involved in]]

[[Category: Relations]] Vanaukenk
Categories: GO Internal

Annotation Conf. Call 2018-03-13

GO wiki (new pages) - Mon, 03/12/2018 - 18:18

Vanaukenk: /* Annotation Review */

= Agenda =
== GOC Meeting, NYU, New York, NY, May 12-14th ==
*Reminder to register, and reserve your hotel room before April 6th if staying at the Shelburne NYC
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Logistics Logistics]
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Agenda Agenda]

== 20th Anniversary GO Meeting, Montreal, CA ==
*Dates set for Oct 17-20

== HTP Annotation Guidelines ==
*Helen has added documentation on the use of HTP evidence codes to the wiki:
**[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Guide to GO Evidence Codes]
**[https://github.com/geneontology/go-annotation/issues/1773 Annotation standards for HTP proteomics experiments]
***How best to capture the combination of a published paper's experiment combined with secondary curator evaluation using some other methodology? New combinatorial evidence code and paper plus a GO reference? (This would be a change to our reference practice.)
**[https://github.com/geneontology/go-annotation/issues/1801 Review RCA evidence code] - Please can the groups listed below review their RCA annotations and decide if they'd still like to keep them and if RCA is still the appropriate evidence code?
***TAIR
***MGI
***SGD
***RGD
***CAFA

== Annotation Review ==
*Annotation review is being driven by annotation QC and ontology development
*Goal here is for correct and consistent annotation
**Prioritize by:
***Annotations that are incorrect
***Annotations to terms that are being made obsolete
***Annotations to high level terms that are not informative
***Annotations to grouping terms for which more granular, informative terms exist (maybe weren't found initially or were created after the annotation was made)
*Tickets are created in the geneontology/go-annotation repo on github
*Currently, 59 open tickets labeled with Annotation Review in geneontology/go-annotation
*Tickets are assigned to representatives of the annotation groups that need to perform the review
*Once review is done, please remove yourself from the assignee list AND record the action in the accompanying Google spreadsheet linked from the github ticket
*[https://drive.google.com/drive/folders/1FDfp4yXlLZjrcB0NIbsAgUukDWDwhJe_ Spreadsheet on GO Annotation Google drive with specific annotations, suggestions]
** Need a re-review of palate development annotations.
*Tickets for discussion:
**[https://github.com/geneontology/go-annotation/issues/1298 HAMAP:MF_03064 mapping for Q9P6N6]
***General issue here: when should we capture a causal relation?
**[https://github.com/geneontology/go-annotation/issues/1746 Review annotations to palate development]
*Some older tickets that still need to be addressed:
**[https://github.com/geneontology/go-annotation/issues/1293 Review annotations to mRNA cleavage]

== Annotation Requests ==
*There are some tickets in geneontology/go-annotation that are requesting annotation
*We'd like to assign these to groups
**[https://github.com/geneontology/go-annotation/issues/1326 Annotating yeast autophagy regulators in PMID:25660547 ?]

= Minutes =
*On call:


[[Category:Annotation Working Group]] Vanaukenk
Categories: GO Internal

Annotation Conf. Call 2018-03-27

GO wiki (new pages) - Mon, 03/12/2018 - 13:14

Vanaukenk:

= Agenda =
== GOC Meeting, NYU, New York, NY, May 12-14th ==
*Reminder to register, and reserve your hotel room before April 6th if staying at the Shelburne NYC
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Logistics Logistics]
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Agenda Agenda]

== 20th Anniversary GO Meeting, Montreal, CA ==
*Dates set for Oct 17-20

== HTP Annotation Guidelines ==
*Helen has added documentation on the use of HTP evidence codes to the wiki:
**[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Guide to GO Evidence Codes]

== Annotation Review ==
*Annotation review is being driven by annotation QC and ontology development
*Goal here is for correct and consistent annotation
**Prioritize by:
***Annotations that are incorrect
***Annotations to terms that are being made obsolete
***Annotations to high level terms that are not informative
***Annotations to grouping terms for which more granular, informative terms exist (maybe weren't found initially or were created after the annotation was made)
*Tickets are created in the geneontology/go-annotation repo on github
*Currently, 55 open tickets labeled with Annotation Review in geneontology/go-annotation
*Tickets are assigned to representatives of the annotation groups that need to perform the review
*Once review is done, please remove yourself from the assignee list AND record the action in the accompanying Google spreadsheet linked from the github ticket
*[https://drive.google.com/drive/folders/1FDfp4yXlLZjrcB0NIbsAgUukDWDwhJe_ Spreadsheet on GO Annotation Google drive with specific annotations, suggestions]
** Need a re-review of palate development annotations.
*Tickets for discussion:
**[https://github.com/geneontology/go-annotation/issues/1298 HAMAP:MF_03064 mapping for Q9P6N6]
***General issue here: when should we capture a causal relation?
**[https://github.com/geneontology/go-annotation/issues/1746 Review annotations to palate development]
*Some older tickets that still need to be addressed:
**[https://github.com/geneontology/go-annotation/issues/1293 Review annotations to mRNA cleavage]

== Annotation Requests ==
*There are some tickets in geneontology/go-annotation that are requesting annotation
*We'd like to assign these to groups
**[https://github.com/geneontology/go-annotation/issues/1326 Annotating yeast autophagy regulators in PMID:25660547 ?]

= Minutes =
*On call:


[[Category:Annotation Working Group]] Vanaukenk
Categories: GO Internal

Software and Utilities Acrhived

GO wiki (new pages) - Fri, 03/09/2018 - 16:29

Cjm: Created page with "Category:Software The purpose of the <b>Software and Utilities</b> group (SWUG) is to support both the GOC and the user community with technical, software, bioinformatics..."

[[Category:Software]]
The purpose of the <b>Software and Utilities</b> group (SWUG) is to support both the GOC and the user community with technical, software, bioinformatics and computer-science related matters. In addition, this group will help drive the GOC through the research and provision of new computational technologies and methodologies relating to ontologies and ontology-based data analysis. This group is responsible for creating, clarifying and extending the common model that underpins all of GO. Ontology development tools are necessary for the [[Ontology Development]] group to perform its function. In addition, the [[Annotation Outreach]] group and wider community need means of exploring and utilizing GO and existing annotations. This group complements all the other groups.

[[Software and Utilities group summary]]

* Timeline: [[SWUG_Timeline_2010-2011]]
* List of projects in progress: [[:Category:SWUG_Projects]]
* [[Software_Group_2010_Future_Plans]]

==Meetings==

See [[:Category:SWUG-TCons]] for all new meetings

*[[SWUG:Meeting_at_Stanford_2011_06_23]]

*[[SWUG:Meeting_2008_04_30]]

*[[SWUG:Meeting_2008_04_16]]

*[[SWUG:Meeting_2008_02_05]]

*[[SWUG:Meeting_2007_12_12]]

*[[SWUG:Meeting_2007_10_17]]

*[[SWUG:Meeting_2007_09_19]] - pre GOC meeting prep

*[[SWUG:Meeting_2007-08-22]]

* Visualisation meeting, 2007-08-16. No notes, demo only

*[[SWUG:Meeting_2007-08-08]]

*[[SWUG:Meeting_2007-07-25]]

*[[SWUG:Meeting_2007-06-27]]

*[[SWUG:Meeting_2007-05-30]]

*[[SWUG:Meeting_2007-04-18]]

*[[SWUG:Meeting_2007-04-04]]

* March 14 2007 -

* [[SWUG:Agenda_Template]]

'''Past Meetings:'''

*[[Database_Meeting_21_Nov_2006]]

'''Forthcoming meetings:'''

Schedule to be decided

*[[SWUG:Topics_for_future_meetings]]

== Reports ==

* [[SWUG:Report_200901]]
* [[SWUG:Database_changes_2007]]

==Mail List==

There is no public mailing list for this group.

==Resources==

===Documentation===

* http://gocwiki.geneontology.org/index.php/GO_FAQ#Software_and_tools
* http://wiki.geneontology.org/index.php/Example_Queries
* http://amigo.geneontology.org/dev
* http://www.geneontology.org/GO.database.shtml
* http://www.geneontology.org/GO.tools.software-libraries.shtml

===Trackers===

* [http://sourceforge.net/tracker/?group_id=36855&atid=934137 GO database]
* [http://sourceforge.net/tracker/?group_id=36855&atid=747782 go-perl]
* [http://sourceforge.net/tracker/?group_id=36855&atid=494390 AmiGO Requests]
* [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports]
* [http://sourceforge.net/tracker/?group_id=36855&atid=418260 Obo-edit requests]
* [http://sourceforge.net/tracker/?group_id=36855&atid=418257 Obo-edit bugs]

===People===

* [[External_Database_Contact_Info]]

===Principles===

* [[SWUG:Quality_Control]]

==Wiki==

All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)

==Projects==

===Galaxy===

[[Galaxy | Everything you need to know about GO Galaxy]]

===OBO-Edit===

*[http://www.oboedit.org OBO-Edit public home page]

*[[OBO-Edit]] wiki page

*[http://wiki.geneontology.org/index.php/Category:OBO-Edit_working_group OBO-Edit working group]

===AmiGO===

====General Interest====

* [[AmiGO_Manual:_Overview]]
* [[AmiGO_Manual:_Installation]]
* [http://sourceforge.net/tracker/?group_id=36855&atid=494390 AmiGO Requests]
* [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports]

====Internal interest====

* [[:Category:AmiGO working group|AmiGO working group]]
* [[AmiGO_Big_Ideas]]
* [[SWUG:AmiGO_Architecture_Roadmap]]
* [[AmiGO]]

===RefGenome===

* [[RG:_Software]]

===TreeCurationTool===

Collaboration with PantherDB

* https://sourceforge.net/projects/pantherdb



===SO===

Main page: http://www.sequenceontology.org

====MiSO====
CVS http://song.cvs.sourceforge.net/song/software/scripts/miSO

browser http://song.sf.net/SO_view/index.html

====Cross-products in SO====

SO contains cross-product definitions of many composite terms. See
[[SO Cross Products]] for the methodology.

===Obol===

http://www.berkeleybop.org/obol

===Reference Genome Software Prototype===

Sohel Merchant has created a prototype as support for the Reference Genome Annotation Project. Currently the project data is managed by means of a google spreadsheet that is difficult to use. The new database and interface will allow the administrator to enter new target genes and for the model organism curators to call their orthologs and to track curation progress of each gene. (For more on the Reference Genome Annotation Project: http://gocwiki.geneontology.org/index.php/Reference_Genome_Annotation_Project )

To access the prototype: http://rails-dev.bioinformatics.northwestern.edu:24000 Cjm
Categories: GO Internal