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 Why not just keep it the same?

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 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 GO Because GO reflects current knowledge

of biology

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 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 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

Growth of GOGO term history 2001 - 2005

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5000

10000

15000

20000

25000

Jan-01Mar-01May-01Jul-01Sep-01Nov-01Jan-02Mar-02May-02Jul-02Sep-02Nov-02Jan-03Mar-03May-03Jul-03Sep-03Nov-03Jan-04Mar-04May-04Jul-04Sep-04Nov-04Jan-05Mar-05

Date

Number of terms

defined terms

undefined terms

obsoletes

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

Original GO:

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 - parasites

Added new term ‘host’:

Example - parasites

parasite gene products located in host nucleus annotated here

parasite gene products located in parasite nucleus annotated here

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

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

Improving GO - example

Editing GO

Logistics file formats DAG-Edit cvs

Communication monthly reports diff emails updating annotations mailing lists

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

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

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 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 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#

defshttp://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

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

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

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

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 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

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

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 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

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 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

Curator requests tracker

Requesting changes to GO - curator requests tracker Common different types of changes suggested:

new term requesthttps://sourceforge.net/tracker/index.php?

func=detail&aid=1207105&group_id=36855&atid=440764

reporting errorshttps://sourceforge.net/tracker/index.php?

func=detail&aid=1206995&group_id=36855&atid=440764

obsoletion/merge requestshttps://sourceforge.net/tracker/index.php?

func=detail&aid=1200109&group_id=36855&atid=440764

add synonymhttps://sourceforge.net/tracker/index.php?

func=detail&aid=1202748&group_id=36855&atid=440764

queries term move

Requesting changes to GO - curator requests tracker Obtaining a SourceForge account demo:https://sourceforge.net/

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 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

average 65.9 new items/month

Tracker volume

24.5 days to complete on average

Other trackers

Listed at:http://www.geneontology.org/GO.sourceforge.links.shtml?

all#track annotation website integrity checks big ideas

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?

Possible topics for discussion: immunology transport/transporters cell cycle signal transduction/signal transducer activity response to/defense terms

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 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

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

Acknowledgements:

The GO Consortium