Gene Ontology Project http://www.geneontology.org/

1. Gene Ontology Project http://www.geneontology.org/

2. Clark et al., 2005 is_a part_of

3. Clark et al., 2005

4. What’s in a GO term?

5. term: fat cell differentiation id: GO:0045444 definition:The process whereby a relatively unspecialized cell acquires specialized features of an adipocyte. An adipocyte is an animal connective tissue cell specialized for the synthesis and storage of fat. exact_synonym: adipose cell differentiation

6. term: fat cell differentiation id: GO:new

7. term: fat cell differentiation id: GO:new definition:The process whereby a relatively unspecialized cell acquires specialized features of an adipocyte. An adipocyte is an animal connective tissue cell specialized for the synthesis and storage of fat.

8. term: fat cell differentiation id: GO:new definition:The process whereby a relatively unspecialized cell acquires specialized features of an adipocyte. An adipocyte is an animal connective tissue cell specialized for the synthesis and storage of fat. exact_synonym: adipose cell differentiation

9. term: fat cell differentiation id: GO:0045444 definition:The process whereby a relatively unspecialized cell acquires specialized features of an adipocyte. An adipocyte is an animal connective tissue cell specialized for the synthesis and storage of fat. exact_synonym: adipose cell differentiation

10. id: GO:0045444 definition:The process whereby a relatively unspecialized cell acquires specialized features of an adipocyte. An adipocyte is an animal connective tissue cell specialized for the synthesis and storage of fat.

11. OBSOLETE: long-day photoperiodism Definition: A change in […] in response to a period of light lasting longer than x hours. New term: long-day photoperiodism Definition: A change in […] in response to a period of darkness lasting shorter than x hours.

13. Spot the odd one out. http://www.nature.com/ncb/journal/v6/n8/images/ncb0804-707-I1.jpg http://animaldiversity.ummz.umich.edu/site/resources/anatomical_images/hair_follicle.jpg http://kyotofly.kit.jp/JDD/bodyparts/thorax_dorsal/acrostichal_hair.gif

14. human hair development http://www.nature.com/ncb/journal/v6/n8/images/ncb0804-707-I1.jpg http://animaldiversity.ummz.umich.edu/site/resources/anatomical_images/hair_follicle.jpg http://kyotofly.kit.jp/JDD/bodyparts/thorax_dorsal/acrostichal_hair.gif

15. plant hair development http://www.nature.com/ncb/journal/v6/n8/images/ncb0804-707-I1.jpg http://animaldiversity.ummz.umich.edu/site/resources/anatomical_images/hair_follicle.jpg http://kyotofly.kit.jp/JDD/bodyparts/thorax_dorsal/acrostichal_hair.gif

16. fly hair development http://www.nature.com/ncb/journal/v6/n8/images/ncb0804-707-I1.jpg http://animaldiversity.ummz.umich.edu/site/resources/anatomical_images/hair_follicle.jpg http://kyotofly.kit.jp/JDD/bodyparts/thorax_dorsal/acrostichal_hair.gif

17. Hare development http://www.nature.com/ncb/journal/v6/n8/images/ncb0804-707-I1.jpg http://animaldiversity.ummz.umich.edu/site/resources/anatomical_images/hair_follicle.jpg http://kyotofly.kit.jp/JDD/bodyparts/thorax_dorsal/acrostichal_hair.gif

18. Sensu hair developent (sensu mammalia) hair developent (sensu magnoliophyta) hair developent (sensu Insecta) organismal developent

19. How is this recorded?

20. gene_ontology.obo [Term] id: GO:0045444 name: fat cell differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat." [GOC:go_curators, http://cancerweb.ncl.ac.uk/] exact_synonym: "adipocyte cell differentiation" [] exact_synonym: "adipocyte differentiation" [] exact_synonym: "adipose cell differentiation" [] is_a: GO:0030154 ! cell differentiation

21. exact_synonym: "DACS" [] exact_synonym: "deacetylcephalosporin C synthetase" [] xref_analog: EC:1.14.11.- is_a: GO:0016706 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors [Term] id: GO:0045443 name: juvenile hormone secretion namespace: biological_process def: "The regulated release of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:go_curators, ISBN:0198547684] is_a: GO:0046879 ! hormone secretion [Term] id: GO:0045444 name: fat cell differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat." [GOC:go_curators, http://cancerweb.ncl.ac.uk/] exact_synonym: "adipocyte cell differentiation" [] exact_synonym: "adipocyte differentiation" [] exact_synonym: "adipose cell differentiation" [] is_a: GO:0030154 ! cell differentiation [Term] id: GO:0045445 name: myoblast differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a cell type that gives rise to mature contractile cells called myocytes. Fusion of myoblasts gives rise to the myotubes that eventually develop into skeletal muscle fibers." [GOC:go_curators, http://cancerweb.ncl.ac.uk/] exact_synonym: "myoblast cell differentiation" [] is_a: GO:0042692 ! muscle cell differentiation relationship: part_of GO:0048741 ! skeletal muscle fiber development [Term] id: GO:0045446 name: endothelial cell differentiation namespace: biological_process

25. The Development Node

26. Terms: 2119 Organism/organ/tissue level [i]x development - 333 ---[p] x morphogenesis - 222 ------[p] x formation - 120 ---------[p] y cell differentiation ------[p] x structural organization - 13 ---[p] x maturation - 7 6th June 2006

27. Cell level [i] y cell differentiation - 351 ---[p] y cell fate commitment - 39 ------[p] y cell fate specification - 63 ------[p] y cell fate determination - 46 ---[p] y cell development - 46 ------[p] y cellular morphogenesis during differentiation - 13 ------[p] y cell maturation - 13

28. Regulation terms [i] y cell differentiation ---[p] regulation of y cell differentiation ------[i] positive regulation of y cell differentiation ------[i] negative regulation of y cell differentiation Development node includes 582 regulation terms.

29. x development The process whose specific outcome is the progression of the x over time, from its formation to the mature structure. [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation zygote http://www.dof.virginia.gov/images/ http://hypertextbook.com/chaos/33.shtml

30. x morphogenesis The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form. [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation http://www.campdevanol.com/blogger/archives/2005_05_01_campdevanol_archive.html

31. x formation The process that gives rise to x. This process pertains to the initial formation of a structure from unspecified parts. [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation Limb bud http://www.sciencemuseum.org.uk/exhibitions/lifecycle/images/1-2-1-2-1-1-0-0-0-0-0.jpg

32. x structural organization The process that contributes to creating the structural organization of x. This process pertains to the physical shaping of a rudimentary structure. [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation http://www.mun.ca/biology/desmid/brian/BIOL3530/DB_Ch05/fig5_20.jpg

33. x maturation A developmental process, independent of morphogenetic (shape) change, that is required for x to attain its fully functional state. [description of x] [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation http://www.dof.virginia.gov/images/

34. y cell differentiation The process whereby a relatively unspecialized cell acquires specialized features of a y cell. [i] y cell differentiation ---[p] y cell fate commitment ------[p] y cell fate specification ------[p] y cell fate determination ---[p] y cell development ------[p] y cellular morphogenesis during differentiation ------[p] y cell maturation http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cmed6.figgrp.41173

35. y cell fate commitment The process whereby the developmental fate of a cell becomes restricted such that it will develop into a y cell. [i] y cell differentiation ---[p] y cell fate commitment ------[p] y cell fate specification ------[p] y cell fate determination ---[p] y cell development ------[p] y cellular morphogenesis during differentiation ------[p] y cell maturation

36. y cell fate specification The process whereby a cell becomes capable of differentiating autonomously into a y cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed. [i] y cell differentiation ---[p] y cell fate commitment ------[p] y cell fate specification ------[p] y cell fate determination ---[p] y cell development ------[p] y cellular morphogenesis during differentiation ------[p] y cell maturation

37. y cell fate determination The process whereby a cell becomes capable of differentiating autonomously into a y cell regardless of its environment; upon determination, the cell fate cannot be reversed. [i] y cell differentiation ---[p] y cell fate commitment ------[p] y cell fate specification ------[p] y cell fate determination ---[p] y cell development ------[p] y cellular morphogenesis during differentiation ------[p] y cell maturation

38. y cell development The process aimed at the progression of a y cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. [i] y cell differentiation ---[p] y cell fate commitment ---[p] y cell development ------[p] y cellular morphogenesis during differentiation ------[p] y cell maturation

39. y cell morphogenesis during differentiation The process by which the structures of a y cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a y cell. [i] y cell differentiation ---[p] y cell fate commitment ---[p] y cell development ------[p] y cellular morphogenesis during differentiation ------[p] y cell maturation http://www.nature.com/ncb/journal/v6/n8/images/ncb0804-707-I1.jpg

40. y cell maturation A developmental process, independent of morphogenetic (shape) change, that is required for a y cell to attain its fully functional state. [description of y] [i] y cell differentiation ---[p] y cell fate commitment ------[p] y cell fate specification ------[p] y cell fate determination ---[p] y cell development ------[p] y cellular morphogenesis during differentiation ------[p] y cell maturation

41. is_a completeness Logically, everything that exists is a sub-type of something else. (There’s a prize if you can think of an exception.)

43. Better searching… Types of limb development: wing development forelimb development hindlimb development tree branch development? fin development? Parts of limb development: limb joint development? limb bone development? limb muscle development?

44. Visualization

45. is_a and part_of is_a

46. The GO Consortium Berkeley Drosophila Genome Project (BDGP) FlyBase GeneDB dictyBase Gene Ontology Annotation @ EBI (GOA) Gramene Mouse Genome Database (MGD) and Reactome Gene Expression Database (GXD) § WormBase Rat Genome Database (RGD) AgBase Saccharomyces Genome Database (SGD) The Arabidopsis Information Resource (TAIR) The Institute for Genomic Research (TIGR) Zebrafish Information Network (ZFIN) GO Editorial Office Candid Genome Database (CGD) HUGO Gene Nomenclature Committee (HGNC) Muscle TRAIT Plant-Associated Microbe Gene Ontology (PAMGO) consortium

47. The GO Consortium