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Only build an ontology if: You have a body of data to annotate.

Only build an ontology if: You have a body of data to annotate. Gene Ontology Consortium. DictyBase. Annotation of Yeast Microarray Clusters Using GO.

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Only build an ontology if: You have a body of data to annotate.

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  1. Only build an ontology if: You have a body of data to annotate.

  2. Gene Ontology Consortium DictyBase

  3. Annotation of Yeast Microarray Clusters Using GO 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.

  4. Only build an ontology if: If you can think of good use cases.

  5. On the representation of "gene function" in databases A discussion paper for ISMB, Montreal, 1998. Version 1.2 -- June 19 1998. • 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.

  6. Only build an ontology if: You have community buy-in or can build that buy-in. BUT: Start small. The difficulty in building an ontology will increase with the square of the number of people involved.

  7. GeneOntology - 1998 FlyBase Drosophila Cambridge, EBI, Harvard Berkeley & Bloomington. SGD Saccharomyces Stanford. MGI Mus Jackson Labs., Bar Harbor.

  8. Flies - Drosophila & GlossinaFlyBase GeneDB Yeasts - Saccharomyces, Schizosaccharomyces & Candida SGD, GeneDB & CGD Mouse - Mouse Genome Database (MGD & GXD) Rat - Rat Genome Database (RGD) Weed - TheArabidopsisInformation 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. Gene Ontology - 2007

  9. Only build an ontology if: Commit to not wasting time on trivia.

  10. Only build an ontology if: If you convince funders to pay for it.

  11. National Institute on Alcohol Abuse and Alcoholism (NIAAA) National Institute on Aging (NIA) National Institute of Allergy and Infectious Diseases (NIAID) National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) National Center for Complementary and Alternative Medicine (NCCAM) National Cancer Institute (NCI) National Institute on Drug Abuse (NIDA) National Institute on Deafness and Other Communication Disorders (NIDCD) National Institute of Dental & Craniofacial Research (NIDCR) National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) National Institute of Biomedical Imaging and Bioengineering (NIBIB) 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) NIH funded experimental research that uses the GO Sample of 77 research papers, both intra-mural & extra-mural research.

  12. Only build an ontology if: You can take criticism.

  13. Only build an ontology if: If you commit to being Open Source and encourage community feedback.

  14. Only build an ontology if: Unless you can make annotated data available as web access as database access as downloadable datasets

  15. Only build an ontology if: You are pragmatic about technical issues.

  16. !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

  17. [ Term ] id: GO:0030183 name: B-cell differentiation is_a: GO:0042113 ! B-cell activation is_a: GO:0030098 ! lymphocyte differentiation intersection_of: is_a GO:0030154 ! cell differentiation intersection_of: has_participant CL:0000236 ! B-cell

  18. [Term] id: SO:0000044 name: pseudogene_by_unequal_crossing_over def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke] is_a: SO:0000336 ! implied link automatically realized ! pseudogene intersection_of: SO:0000336 ! pseudogene intersection_of: has_quality SO:0000901 ! unequally_crossed_over relationship: has_quality SO:0000901 ! implied link automatically realized ! unequally_crossed_over

  19. Only build an ontology if: If you can commit to using the Relations Ontology.

  20. Only build an ontology if: You can commit to (re)-use community tools.

  21. Only build an ontology if: You are or are deemed to be “a person overly obsessed with minor details.” (WikiPedia).

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