Only build an ontology if:

You have a body of data to annotate.

Gene Ontology Consortium

DictyBaseQuickTime™ and aTIFF (LZW) decompressorare needed to see this picture.

Microarray data from Figure 2K of Eisen et al. (1998). Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. 95 (25): 14863-14868.

Annotation of Yeast Microarray Clusters Annotation of Yeast Microarray Clusters Using GOUsing GO

ORF NAME GENE PROCESS FUNCTION CELLULAR COMPONENTYNL055C POR1 other anion transport voltage-gated ion channel mitochondrial outer membraneYGR194C XKS1 xylulose metabolism xylulokinase cytoplasmYKL148C SDH1 tricarboxylic acid cycle succinate dehydrogenase mitochondrial inner membraneYML120C NDI1 oxidative phosphorylation NADH dehydrogenase mitochondrial inner membraneYDR529C QCR7 electron transport ubiquinol--cytochrome-c reductase mitochondrial inner membraneYHR051W COX6 oxidative phosphorylation cytochrome-c oxidase mitochondrial inner membraneYEL024W RIP1 electron transport Rieske Fe-S protein mitochondrial inner membraneYER141W COX15 oxidative phosphorylation cytochrome-c oxidase mitochondrial inner membraneYOR065W CYT1 electron transport cytochrome-c1 mitochondrial inner membraneYBL045C COR1 electron transport ubiquinol--cytochrome-c reductase mitochondrial inner membraneYKL141W SDH3 tricarboxylic acid cycle

electron transportsuccinate dehydrogenase subunit mitochondrial inner membrane

YDR178W SDH4 tricarboxylic acid cycleelectron transport

succinate dehydrogenase subunit mitochondrial inner membrane

YLL041C SDH2 tricarboxylic acid cycleelectron transport

succinate dehydrogenase subunit mitochondrial inner membrane

YKL085W MDH1 tricarboxylic acid cycle malate dehydrogenase mitochondrial matrixYFR033C QCR6 electron transport ubiquinol--cytochrome-c reductase mitochondrial inner membraneYOR065W CYT1 electron transport cytochrome-c1 mitochondrial inner membraneYBL015W ACH1 acetyl-CoA metabolism acetyl-CoA hydrolase cytoplasm

Only build an ontology if:

If you can think of good use cases.

•where is a gene expressed? the spatial problem,described in terms of an organism's anatomy.

•what is the (sub)-cellular localisation of a gene product?,described in terms of subcellular anatomy.

•when is a gene expressed? the temporal problem,described interms of an organism's ontogeny.

•what is the function of a gene product?,described in terms of a functional classification of gene products.

•of what larger process is the function of a gene's product a part?,described in terms of a process hierarchy.

•by what processes is a gene's activities controlled ?•what genes does a gene's product regulate ?,

described by a regulatory hierarchy.•of what larger complex is this function a component?,

described by a parts-list of multi-component (RNA, protein, etc) complexes.•what genes in species a have the function of gene x in species b?

represented by species a and b sharing a functional classification of gene products, with the necessary links between the databases.

On the representation of "gene function" in databases

A discussion paper for ISMB, Montreal, 1998.Version 1.2 -- June 19 1998.

Only build an ontology if:

You have community buy-in or can build that buy-in.

BUT: Start small. The difficulty in building an ontologywill increase with the square of the number of peopleinvolved.

Gene Ontology - 1998

FlyBase Drosophila Cambridge, EBI, HarvardBerkeley & Bloomington.

SGD Saccharomyces Stanford.

MGI Mus Jackson Labs., Bar Harbor.

Gene Ontology - 2007• Flies - Drosophila & Glossina FlyBase GeneDB• Yeasts - Saccharomyces, Schizosaccharomyces & Candida SGD, GeneDB

& CGD• Mouse - Mouse Genome Database (MGD & GXD)• Rat - Rat Genome Database (RGD)• Weed - The Arabidopsis Information Resource (TAIR)• Worm - WormBase• Dictyostelium - Dictybase• InterPro/UniProt at EBI - InterPro• Human - UniProt, Ensembl, NCBI, Incyte, Celera, Compugen• Parasites - Plasmodium, Trypanosoma, Leishmania - GeneDB• Microbes - Vibrio, Shewanella, B. anthracus, … - TIGR• Grasses - rice & maize - Gramene database• zebra fish - Zfin• Chicken, cow - Agbase• Tetrahymena - Tetrahymena DataBase (TGD)• Coming: Xenopus, Aspergillus, Chlamydomonas, & more.

Only build an ontology if:

Commit to not wasting time on trivia.

Only build an ontology if:

If you convince funders to pay for it.

NIH funded experimental research that uses the GO

1. National Institute on Alcohol Abuse and Alcoholism (NIAAA)

2. National Institute on Aging (NIA)3. National Institute of Allergy and

Infectious Diseases (NIAID)4. National Institute of Arthritis and

Musculoskeletal and Skin Diseases (NIAMS)

5. National Center for Complementary and Alternative Medicine (NCCAM)

6. National Cancer Institute (NCI)7. National Institute on Drug Abuse (NIDA)8. National Institute on Deafness and Other

Communication Disorders (NIDCD)9. National Institute of Dental & Craniofacial

Research (NIDCR)10. National Institute of Diabetes and

Digestive and Kidney Diseases (NIDDK)11. National Institute of Biomedical Imaging

and Bioengineering (NIBIB)12. National Institute of Environmental Health

Sciences (NIEHS)

13. National Eye Institute (NEI)

14. National Institute of General Medical Sciences (NIGMS)

15. National Institute of Child Health and Human Development (NICHD)

16. National Human Genome Research Institute (NHGRI)

17. National Heart, Lung and Blood Institute (NHLBI)

18. National Library of Medicine (NLM)

19. National Center on Minority Health and Health Disparities (NCMHD)

20. National Institute of Mental Health (NIMH)

21. National Institute of Nursing Research (NINR)

22. National Institute of Neurological Disorders and Stroke (NINDS)

23. National Center for Research Resources (NCRR)

24. Fogarty International Center (FIC)

Sample of 77 research papers, both intra-mural & extra-mural research.

Only build an ontology if:

You can take criticism.

Only build an ontology if:

If you commit to being Open Sourceand encourage community feedback.

Only build an ontology if:

Unless you can make annotated data availableas web accessas database accessas downloadable datasets

Only build an ontology if:

You are pragmatic about technical issues.

!version: $Revision: 1.113 $!date: $Date: 2000/12/22 17:46:17 $!editors: Michael Ashburner (FlyBase), Midori Harris (SGD), Judith Blake (MGD)$Gene_Ontology ; GO:0003673 $cellular_component ; GO:0005575 %membrane ; GO:0016020 <integral membrane protein ; GO:0016021 %cell fraction ; GO:0000267 %insoluble fraction ; GO:0005626 %membrane fraction ; GO:0005624 %soluble fraction ; GO:0005625 %cell wall ; GO:0005618 <periplasmic space ; GO:0005620 %cell wall (sensu Fungi) ; GO:0009277 % extracellular ; GO:0005576 %cell wall (sensu Bacteria) ; GO:0009274 ; synonym:envelope (sensu Bacteria) % extracellular ; GO:0005576 <cell wall inner membrane ; GO:0009280 ; synonym:cytoplasmic membrane % membrane ; GO:0016020 <Type II protein (Sec) secretion system complex ; GO:0015627 <murein sacculus ; GO:0009278 ; synonym:capsule <cell wall outer membrane ; GO:0009279 % membrane ; GO:0016020 %cell wall (sensu gram-positive Bacteria) ; GO:0009275 %cell wall (sensu gram-negative Bacteria) ; GO:0009276 %cell wall (sensu Magnoliophyta) ; GO:0009505 < cell ; GO:0005623 %spore wall (sensu Fungi) ; GO:0005619 < ascus ; GO:0005627 <bud scar ; GO:0005621

[ Term ]id: GO:0030183name: B-cell differentiationis_a: GO:0042113 ! B-cell activationis_a: GO:0030098 ! lymphocyte differentiationintersection_of: is_a GO:0030154 ! cell differentiationintersection_of: has_participant CL:0000236 ! B-cell

[Term]id: SO:0000044name: pseudogene_by_unequal_crossing_overdef: "A pseudogene caused by unequal crossing over at recombination." [SO:ke]is_a: SO:0000336 ! implied link automatically realized ! pseudogeneintersection_of: SO:0000336 ! pseudogeneintersection_of: has_quality SO:0000901 ! unequally_crossed_overrelationship: has_quality SO:0000901 ! implied link automatically realized ! unequally_crossed_over

Only build an ontology if:

If you can commit to using the Relations Ontology.

Only build an ontology if:

You can commit to (re)-use community tools.

Only build an ontology if:

You are or are deemed to be “a person overly obsessed with minor details.” (WikiPedia).