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Modifying GO. How changes are made to GO, and how you can be involved. Modifying GO:. Why we have to make changes to GO How changes are made to GO The GO editorial office How you can make changes to GO SourceForge Interest groups Content meetings. Why we have to make changes to GO.

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Modifying go

Modifying GO

How changes are made to GO, and how you can be involved


Modifying go1
Modifying GO:

  • Why we have to make changes to GO

  • How changes are made to GO

  • The GO editorial office

  • How you can make changes to GO

    • SourceForge

    • Interest groups

    • Content meetings


Why we have to make changes to go
Why we have to make changes to GO

  • Why not just keep it the same?


Why we have to make changes to go1
Why we have to make changes to GO

  • Why not just keep it the same?

    • annotations would never need fixing


Why we have to make changes to go2
Why we have to make changes to GO

  • Why not just keep it the same?

    • annotations would never need fixing

    • wouldn’t need an editorial office


Why we have to make changes to go3
Why we have to make changes to GO

  • Because GO reflects current knowledge of biology


Why we have to make changes to go4
Why we have to make changes to GO

  • Because GO reflects current knowledge of biology

    • biology always changing


Why we have to make changes to go5
Why we have to make changes to GO

  • Because GO reflects current knowledge of biology

    • biology always changing

  • New organisms being added makes existing terms arrangements incorrect

    • we generally only add terms in response to annotation needs

    • if organism not being annotated, terms won’t be present in GO


Why we have to make changes to go6
Why we have to make changes to GO

  • Because GO reflects current knowledge of biology

    • biology always changing

  • New organisms being added makes existing terms arrangements incorrect

    • we generally only add terms in response to annotation needs

    • if organism not being annotated, terms won’t be present in GO

  • Not everything perfect from the outset



Evolution of go
Evolution of GO

  • Original GO

    • FlyBase (Drosophila)

    • MGI (Mouse)

    • SGD (S. cerevisae)

  • Later

    • TAIR (Arabadopsis)

    • TIGR (microbes including prokaryotes)

    • SWISS-PROT (several thousand species inc. human)

    • PSU (P. falciparum)

  • Recent additions

    • PAMGO (plant pathogens)


Example parasites
Example - parasites

  • Original GO:


Example parasites1
Example - parasites

  • Annotation of P. falciparum

    • protozoan cellular parasite

    • intracellular infection (erythrocytes)

  • Parasite proteins located in host nucleus

  • What cellular component term to annotate to?

    • ‘nucleus’ refers to parasite nucleus when annotating parasite


Example parasites2
Example - parasites

  • Added new term ‘host’:


Example parasites3
Example - parasites

parasite gene products located in parasite nucleus annotated here

parasite gene products located in host nucleus annotated here


Improving go
Improving GO

  • Some parts of GO need expanding/improving

  • In progress:

    • immunology

    • cell cycle

    • development

    • fungal toxin metabolism

  • Still to do:

    • transporters and transport

    • signal transducer/signalling pathways


Improving go example
Improving GO - example

  • Interactions between organisms

    • e.g. symbiosis, host/pathogen interaction, biofilm formation

  • Not well covered in GO

    • very few terms

    • some inconsistencies

  • PAMGO developed node last year



Editing go
Editing GO

  • Logistics

    • file formats

    • DAG-Edit

    • cvs

  • Communication

    • monthly reports

    • diff emails

    • updating annotations

    • mailing lists


Editing go file formats
Editing GO - file formats

  • GO available in different formats:

    • OBO flat file (terms & definitions only)

    • GO flat file (terms & definitions only)

    • XML (terms & definitions only)

    • OWL (terms & definitions only)

    • MySQL (terms, definitions & annotations)

  • OBO flat file primary editing format for ontologies


Go file formats
GO file formats

  • Different formats different update times:

    • OBO flat file: every 30 minutes

    • GO flat file, XML, OWL: daily

    • MySQL: weekly without IEAs, monthly with IEAs

  • AmiGO runs from MySQL database so will not show new terms immediately

  • QuickGO updates weekly


Editing go dag edit
Editing GO - DAG-Edit

  • Generic ontology editing tool developed by GO consortium

  • Java-based stand-alone tool

  • Used to do almost all ontology edits

  • demo

  • Downloading DAG-Edit:

    http://sourceforge.net/project/showfiles.php?group_id=36855

  • DAG-Edit help:

    http://www.godatabase.org/dev/java/dagedit/docs/index.html


Editing go example adding new term
Editing GO example: adding new term

  • Suggestion of new term from annotator:

    • Check whether term exists under another name

      • search terms and synonyms

    • Determine if valid GO term

      • e.g. disease process, individual gene products not allowed

    • Decide on placement in ontology


Editing go example adding new term1
Editing GO example: adding new term

  • Write definition if not provided

    • from biological dictionaries, experts, papers, online sources

    • some types of terms e.g. metabolism have standardised definitions, see:

      http://www.geneontology.org/GO.function.guidelines.shtml?all#defs

      http://www.geneontology.org/GO.process.guidelines.shtml

  • Add term with new id in DAG-Edit

  • Inform annotator of new term name and id


Editing go cvs
Editing GO - cvs

  • Amended ontology file committed to cvs (concurrent versions system) repository located at Stanford

  • cvs prevents changes being overwritten by other editors

  • Allows files to be reverted to former versions

  • log files detailing changes

  • Anonymous cvs available:

    http://www.geneontology.org/GO.downloads.shtml?all#cvs


Editing go monthly reports
Editing GO - monthly reports

  • Every month a full report released with all changes made to ontologies that month:

    http://www.geneontology.org/MonthlyReports/

  • Generated with set of Perl scripts available on GO FTP site

  • Includes:

    • new terms

    • term name changes

    • new definitions

    • term movements

    • term obsoletions

    • SF items closed

    • overall statistics


Editing go diff files
Editing GO - diff files

  • Daily email with all changes made to file that day

  • Subscribe to go-diff mailing list:

    http://www.geneontology.org/GO.mailing.lists.shtml?all#godiff

  • Example diff:


Mailing lists
Mailing lists

  • Several GO mailing lists:

    • GO (main)

      • discussion of ontology development

      • general queries/error reporting

      • high-traffic

    • GO-friends

      • mainly announcements

      • low-traffic

    • annotation

      • all annotation issues

    • GO-diff

    • GO-database

      • all database/techy issues


Mailing lists1
Mailing lists

  • All mailing lists archived:

    http://www.geneontology.org/GO.contents.archives.mail.shtml?all

  • Subscribe:

    http://www.geneontology.org/GO.mailing.lists.shtml

  • Interest group mailing lists


Editing go updating annotations
Editing GO - updating annotations

  • Annotations become out-of-sync with ontologies

    • term name changes

    • term obsoletions

    • term merges

  • Databases have individual strategies for flagging

  • 2 week notice given on obsoletions, provided no objections

  • Example email:

    http://www.geneontology.org/email-go/go-arc/go-2005/0012.html


The go editorial office
The GO editorial office

  • Located at European Bioinformatics Institute, Cambridge UK

  • Four full-time editors of the ontologies:

    • Midori Harris

    • Jane Lomax

    • Amelia Ireland

    • Jennifer Clark


The go editorial office1
The GO editorial office

  • Primary responsibility to edit ontologies in response to community needs

  • Also:

    • website

    • documentation

    • outreach

      • GO in other systems

      • new annotation groups

    • training


Requesting changes to go
Requesting changes to GO

  • Curator requests tracker

    • demo of how to add an item

    • types of changes

      • new terms

      • errors - tpvs

      • obsolete terms

  • Interest groups

  • Content meetings


Requesting changes to go curator requests tracker
Requesting changes to GO - curator requests tracker

  • Web-based tracking system hosted at SourceForge.net

  • Tracker item for each new request or question

  • Allows requests/suggestions/comments to be added by anyone

  • Daily digest of new tracker items goes to GO mailing list



Requesting changes to go curator requests tracker1
Requesting changes to GO - curator requests tracker

  • Common different types of changes suggested:

    • new term request

      https://sourceforge.net/tracker/index.php?func=detail&aid=1207105&group_id=36855&atid=440764

    • reporting errors

      https://sourceforge.net/tracker/index.php?func=detail&aid=1206995&group_id=36855&atid=440764

    • obsoletion/merge requests

      https://sourceforge.net/tracker/index.php?func=detail&aid=1200109&group_id=36855&atid=440764

    • add synonym

      https://sourceforge.net/tracker/index.php?func=detail&aid=1202748&group_id=36855&atid=440764

    • queries

    • term move


Requesting changes to go curator requests tracker2
Requesting changes to GO - curator requests tracker

  • Obtaining a SourceForge account

  • demo:

    https://sourceforge.net/


Requesting changes to go curator requests tracker3
Requesting changes to GO - curator requests tracker

  • Submitting a request

  • demo:

    https://sourceforge.net/tracker/?atid=440764&group_id=36855&func=browse


Requesting changes to go curator requests tracker4
Requesting changes to GO - curator requests tracker

  • Things to bear in mind when submitting a request:

    • Have you given us enough information?

      • useful things to include are references to papers, name/id of gene being annotated, EC numbers

      • if you’re requesting an e.g. obsoletion or merge, have you put a reason?

    • Have you included a definition?

      • very useful where requests very organism-specific or if you’re an expert

      • source of definition, PubMed id, ISBN etc.

    • Are there any synonyms you would like included for a new term? What type?

      • synonym types are exact, broader and narrower

    • Have you suggested parentage for a new term?


Tracker volume
Tracker volume

  • average 65.9 new items/month


Tracker volume1
Tracker volume

  • 24.5 days to complete on average


Other trackers
Other trackers

  • Listed at:

    http://www.geneontology.org/GO.sourceforge.links.shtml?all#track

    • annotation

    • website

    • integrity checks

    • big ideas


Content meetings
Content meetings

  • Short meetings aimed at developing specific areas of GO ontology content

    • proposals defined and discussed before meeting

    • small number of people

    • invited experts

    • specific topics


Next content meeting november
Next content meeting - November?

  • Possible topics for discussion:

    • immunology

    • transport/transporters

    • cell cycle

    • signal transduction/signal transducer activity

    • response to/defense terms


Interest groups
Interest groups

  • Groups of experts for a specific topic

    • e.g. development, cell cycle, plants

  • Includes GO curators/annotators and external experts

  • Communicate by mailing lists and at meetings


Interest groups1
Interest groups

  • We actively encourage annotators to join interest groups for their field

  • Complete list of groups:

    http://www.geneontology.org/GO.interests.shtml?all


Go documentation
GO documentation

  • Much documentation:

    http://www.geneontology.org/GO.contents.doc.shtml


Acknowledgements:

The GO Consortium


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