Difference between revisions of "Isa-complete BP"
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'anatomical structure development' (GO:0048856); many could probably be moved further down to be
'anatomical structure development' (GO:0048856); many could probably be moved further down to be
children of new or existing children of GO:0048856.
children of new or existing children of GO:0048856.
Also see additions to to-do list.
Also see additions to to-do list.
Revision as of 05:32, 10 October 2006
Notes on making the biological process ontology is_a complete
- 1 Seattle working sessions Sept. 8-9, 2006
- 2 Hinxton working sessions Oct. 2-3, 2006
- 3 To-do list
Seattle working sessions Sept. 8-9, 2006
David Hill, Jane Lomax, Jen Clark, Tanya Berardini
1. Ensure that each term in the BP ontology has a path to the root that passes solely through is_a parent-child relationships.
2. Clarify the difference between BP terms that represent collections of processes and BP terms that represent a specific, entire process. Right now, there are terms of the form “xx process” that are either one or the other.
3. Refine definitions, term-term relationships as they are encountered.
4. Check for redundant relationships using OBO-Edit reasoner plug-in and resolve them.
5. Calculate number of is_a orphans before and after (should be zero) editing process.
Rules we tried to adhere to
1. Metabolic process is defined as a collection of processes. Therefore, is_a children of metabolic process can be specific metabolic processes.
2. Cell division terms should be children of the related cell proliferation terms.
Example: Endothelial cell division is part of endothelial cell proliferation.
COMMENT: Double-check this in light of the long discussions about cell division vs. cell proliferation that we've had in the past. X cell division part_of X cell proliferation is probably fine where X cell is some kind of cell in a multicellular organism tissue, but there has been resistance to making the relationship between the generic parents. See SF 1219649 and this thread in the email archive for many gory details. (MAH)
3. A term should not be an is_a child of two top level granularity terms but it can be an is_a of one and a part_of the other.
Example: A term can be an is_a cellular and part of organismal but not an is_a of both cellular and organismal.
4. Define each specific process as having a discrete beginning and end.
5. regulation of xx process and is_a vs. part_of relationship to xx process: It can be an is_a child if the parent is a collection of processes in which any instance of the regulation of a process is an instance of the parent. If the parent process is a specific process and an instance of the regulation is not a complete instance of the parent but rather contributes to an instance of the parent's whole then the regulation is a part_of that process. (Verbatim quote from DH.)
6. Sometimes a parent can have only an is_a relationship but its is_a children can have part of relationships to other parents.
Example: sex determination, mating type determination (part of ?) , female sex determination (part of multicellular organismal development).
7. A term can be a part of organismal development and is_a cell development.
Example: dopaminergic neuron development is_a cell development and part_of multicellular organismal development
8. For BP process terms that refers to a collection of processes, use this string “xxx biological process” or "xxx process"
Example: metabolism becomes ‘metabolic biological process’ and 'developmental process'. The distinction is still vague because all types represent collections, but the idea is that more generic processes will be distinguished in this way.
Potential top level terms under biological process
Molecular process: rejected because that's what the function ontology represents
Subcellular process: rejected because cellular is going to include the level of the cell and below
Cellular process: accepted (cellular includes single celled organisms)
Multi-cellular process: considering but transformed into organismal (multi-cellular organismal process
Tissue process: will probably included under multi-cellular organismal
Organ process: under development only
Organismal process: accepted but called multi-cellular organismal process (see above) , for our purposes, single celled organisms = cells. Single-celled organisms will be included in this group.This gets around the nasty confusion when we refer to organismal.
Population: too far, someone should do it but not us (Jane in a former life)
Notes from the discussions
1. We did not create separate terms for 'development' and 'developmental process' because their definitions would essentially be the same. If we want to use development to refer to the development of XXX then we will create that specific XXX development term. We don't need a generic term for binning purposes only.
Example: Cell development is_a developmental process.
2. We need to be very clear about what's happening at the level of the cell and what is happening at the level of the tissue.
Examples: meristem vs. meristem cell
Cell migration vs. cell motility
Cell division vs. cell proliferation
3. Cell development and cell developmental process are different things.
4. Many terms that were is_a organismal development were made part_of organismal development and is_a developmental process. This is not a hard and fast rule because some of these children terms need to go to deeper terms than organismal development.
5. Problems arise from single cell organisms = organisms. Therefore, we’ve gone with single cell organisms = cell.
6. We don't want to have cell types of single celled organisms.
7. We touched areas pertaining to the following Sourceforge items:
a. Hatching – can now make different types: blastocyst hatching, avian hatching (would be a behavior)
b. somatic embryogenesis (fixed embryonic development definition)
c. meristem/stem cell population maintenance
8. Cell division was not made an is_a child of cellular reproduction.
Proposed Ontology changes (some implemented in the working draft)
1. New terms added: (note: ids are temporary and will change upon final implementation)
GO:0048856 multicellular organismal process
GO:0048857 developmental process
GO:0048858 meristem cell maintenance
GO:0048859 multicellular organism reproduction
GO:0048860 cellular reproduction
GO:0048861 shoot system development
GO:0048862 root system development
GO:0048863 stem cell differentiation
GO:0048864 stem cell development
GO:0048865 stem cell fate commitment
GO:0048866 stem cell fate specification
GO:0048867 stem cell fate determination
GO:0048868 pollen tube development
GO:0048869 cellular developmental process
GO:0048870 cell motility involved in cell locomotion
GO:0048871 multicellular organismal homeostasis
GO:0048872 homeostasis of number of cells
GO:0048873 homeostasis of number of cells within a tissue
GO:0048874 homeostasis of number of cells in a free-living population
GO:0048875 chemical homeostasis within a tissue
GO:0048876 retinal chemical homeostasis
GO:0048877 homeostasis of number of retinal cells
GO:0048878 chemical homeostasis
2. Terms merged
merged organismal physiological process ; GO:0050874 into multicellular organismal process ; GO:0048856
merged reproductive physiological process ; GO:0050876 into reproduction ; GO:0000003
merged physiological process ; GO:0007582 into biological_process ; GO:0008150
merged cellular physiological process ; GO:0050875 into cellular process ; GO:0009987
3. First iteration of Homeostasis – renamed as homeostatic (biological) process
--Homeostatic process (related synonym: homeostasis; set of homeostatic processes ??) ----[i]organismal homeostasis ----[i]cell homeostasis ----[i]cell number homeostasis ------[i]cell number homeostasis within a tissue ------[i]free living cell number homeostasis ----[i]tissue homeostasis ------[p]cell number homeostasis in a tissue ------[?]tissue metabolic homeostasis
4. ‘development of anatomical structure’
--developmental process ----[i]development of anatomical structure (GO:new!)- apparently, this term is still under discussion (Doug, Cindy Smith) ------[i] nerve development ------[i] reproductive structure development ------[i] tube development
5. May want to make a term 'cell division of a single celled organism' and make that a synonym of cellular reproduction.
6. May want 'multicellular organismal sex determination' and 'single cell sex determination' for grouping. Possibly also 'multicellular organismal sex development'.
7 . May need stem cell development. Look at all part of children and see if they can be grouped under a single is_a parent. –Done: stem cell differentiation and related children added. (see terms added above)
1. TO LIST: Should reproductive structure development be a part_of reproduction or not? If not, we should add onto the definition of reproduction that this does not include the development of the reproduction structures. Will reproduction start with embryogenesis and development of the reproductive structure? Does the reproductive process begin before or after the formation (maturation?) of the reproductive structures? (Similarly is development of the eye a part of visual perception?)
COMMENT: This is clearly madness. Reproductive structures are necessary for reproduction, and hence their (correct) development is necessary for reproduction. There is obviously a relationship but I think it's not "part_of". Would you say "sight" is part_of "reproduction" when the lights are on? OK, I am being silly - but what I am trying to say is that not every relationship can (or should) be captured with is_a and part_of. - BEN
COMMENT: I'm beginning to agree that these should be split even if a mutant phenotype can't necessarily distinguish between the two. Perhaps at some point the connection can be made via annotations.-DPH
2. Do we need regulatory process in addition to regulation?
COMMENT: I think regulation of biological process will cover these is_a paths. THe regulation terms make the graph complicated with respect to multiple is_a parentages. Perhaps the intorduction of the regulates relationship will help this. For now we didn't deal with regulation terms. -DPH
3 Do we need a higher level term: cell population process?
COMMENT: Currently terms like 'cell migration' and 'cell proliferation' refer to populations of cells. Currently cellular process can include processes that occur in more than one cell but at the cellular level, for example 'cell signaling'. I think we are o.k. because when we talk about these population issues, we are almost always talking about a homogeneous group of cells. -DPH
4. Tissue homeostasis relationship to organismal homeostasis: part of vs. is_a? Should it just be is_a homeostasis and its children should be children of organismal homeostasis?
COMMENT: I thought we had resolved this in the draft graph. Tissue homeostasis referred to the steady state level of cells in a tissue, but other homeostasis terms refered to chemical levels. I think I remember us splitting this out. -DPH
5. Should intracellular signaling cascade, or its parent signal transduction, be is_a cellular physiological process? See SF 1558514.
Hinxton working sessions Oct. 2-3, 2006
David Hill, Jane Lomax, Jen Clark, Midori Harris
1) Used OBO-Edit filters to identify "is_a orphans," i.e. terms that didn't have at least one all-is_a path
2) Went through orphans one by one to find is_a parent(s); created some new grouping terms, and will probably add more (see below)
3) Used OBO-Edit reasoner to detect redundant links and resolved them.
4) Made plans for completing the work via Webex [or equivalent]
a) Jane and Jen will do the first pass to look at the remaining is_a orphans and create relationships for the straightforward ones.
b) Save any problematic ones for a Webex session
c) Also via Webex: for each high-level term, look at children and add grouping terms as needed, esp. if there are a lot of children and/or 'natural' groupings are obvious
More on 3c: For the work during and immediately after the meeting, we decided to add high-level is_a parents for now, and to go back to each high-level term to see whether the children should be grouped further. For example, we stuffed a lot of development terms directly under 'anatomical structure development' (GO:0048856); many could probably be moved further down to be children of new or existing children of GO:0048856.
5) Once Jane/Jen and the rest of the group have made is_a paths for the remaining orphans, we will have a 'round robin' editing session similar to the ones we did for CNS. Each person in the group will work on th ontology for a week, refining children and relationships in an area of the graph. Areas needing attention will be development, metabolism, movement/localization and other areas with large numbers of direct is_a children. At the end of each week, the working graph will be forwarded to Jane and she will merge it with the live GO to keep things in synch.---[dph;10/10/2006]
Also see additions to to-do list.
Rules, rationales, clever ideas
1. Insight from the cell cycle: 'X cycle process'
--cell cycle ----[p] cell cycle process ------[i] cell cycle phase (e.g. M phase) ----[p] cell cycle phase (e.g. M phase)
--cellular process ----[i] cell cycle --[i] cell cycle process
In other words, a cell cycle process (or can think of it as a cell cycle subprocess) is a process that forms part of the cell cycle
Any other cycle can be treated the same way; the parent of 'X cycle process' will be either cellular process (GO:0009987) or multicellular organismal process (GO:0032501), as appropriate. Furthermore, this approach can also be applied to non-cyclical processes!
2. Development, developmental process - handle as for cell cycle, i.e.
--biological process --[i] development ----[p] developmental process --[i] developmental process
There was much discussion of whether the existing 'development' term (GO:0007275) should remain 'development' (i.e. the e complete developmental program of any organisms; the whole process), 'developmental process' (a collection of processes involved in development), or 'multicellular organismal development' (as for 'development', but excluding single-celled organisms. (Note that there was never any doubt that we want all of these terms; the question was which one we already have.) Despite the fact that option 3 (multicellular organismal development) is the name GO:0007275 has in the final IsaComplete.obo file from the meeting, Midori votes for GO:0007275 to be 'development', and for 'developmental process' to get a new ID, because there is less risk of any existing annotations going wrong. There are two S. pombe gene products annotated directly to GO:0007275!
Whichever way we do it, the current children of GO:0007275 will have to be examined to see which ones should go under 'developmental process and which under multicellular organismal development (also see to-do list).
3. Morphogenesis is equivalent to morphogenesis of an anatomical structure, so we don't need two separate terms. note, however, that we do need separate terms for 'development' and 'anatomical structure development' because (a) 'development' includes both morphogenesis and maturation, and (b) development of an anatomical structure can be distinguished from development of an entire organism.
Anatomical structure development is_a developmental process.
Morphogenesis is_a developmental process, and part_of anatomical structure development.
For GO's purposes, define 'anatomical structure' as part of an organism (note: FMA has organism is_a anatomical structure).
4. We'll also have reproduction and reproductive process:
--biological process ----[i] reproduction ------[p] reproductive process ----[i] reproductive process
Much discussion of how cellular reproduction (GO:0032505) should relate to reproductive cellular process (GO:0048610); result was to keep both, refine defs, rename GO:0032505 to 'reproduction of a single-celled organism', and add two children to GO:0048610, 'reproductive process in single-celled organism' and 'reproductive cellular process in multicellular organism'.
5. Metabolism, metabolic process, & transport
We'll do the same again (though it's not done yet) ...
--biological process ----[i] metabolism ------[p] metabolic process ----[i] metabolic process
Note that the existing term, GO:0008152, will become 'metabolic process' because we've used it with essentially that meaning, i.e. a collection of processes.
Now that 'X metabolism' terms are defined as 'The chemical reactions and pathways involving X', perhaps we can make X transport a child of X metabolism ... an idea for further discussion. We would NOT make transport of anything other than X itself (precursors 7 whatnot) a child of X metabolism.
6. We're proposing to obsolete 'establishment of dosage compensation' (GO:0007550) because (a) it's undefined; (b) it's not used for annotations; and, most importantly, (c) it seemed to us that there are several different mechanisms of dosage compensation that do not have an establishment mechanism in common. It would be better to have specific terms for establishment of each kind of dosage compensation that are parts of the respective dosage compensation processes and is_a children of the type of process. For example, establishment of dosage compensation by Barr body formation is a type of heterochromatin formation. Also see to-do list.
7. A handy way to tell if a process term should be is_a or part_of its parent: ask whether an instance of the child is an instance of the entire process? If yes, the child is is_a; but if it's an instance of only a portion of the parent process, the child is part_of.
1. What was the reason for naming GO:0042065 'glial growth' rather than 'glial cell growth'? Can it be renamed and made is_a cell growth?
2. What does 'absorption of light' (GO:0016037) really mean? The current def ('The reception of a photon by a cell.') is not very helpful, and we couldn't think of an Aristotelian one ...
3. Is a hair follicle an organ?
4. Should we have a generic 'regulation' term? (If so, it would have two children - regulation of biological process and regulation of a trait.)
5. Will we want 'cell-cell docking'? How similar are the molecules involved in, say, conjugant formation and [some other example]?
6. Should 'reproduction of a single-celled organism' be under reproduction (at present it is)? Or is it just cell division? Biologists would expect to find single-celled organism reproduction under reproduction!
7. Do we have 'elongation' under 'growth'? [answer: no; the closest thing is unidimensional cell growth, GO:0009826, which is_a cell growth and has 'cell elongation' as a narrow synonym]
8. Can establishment of dosage compensation' (GO:0007550) be defined sensibly, and given an is_a parent, or should we go ahead with the proposed obsoletion? Ask Michael about dosage compensation generally.
8 COMMENT: Also see SourceForge item 1569608, on the component term 'dosage compensation complex'. (midori 10-10-06)
9. What does 'establishment of synaptic specificity at neuromuscular junction' (GO:0007529) really mean? Does it refer to which neurotransmitter is used? Ask Erika.
10. Should we have four types of 'follicular fluid formation in ovarian follicle antrum'? At present GO:0001548 is part_of four different parent processes.
11. Can the 'formation of catalytic spliceosome ...' terms (GO:0000349 & GO:0000350) be renamed to avoid saying 'formation'? The 'formation' wording made us think of protein (or RNP) complex assembly, but the terms describe conformational changes. Also, does the protein folding parentage make sense? Ask Karen C.
12. Does 'formation of generative and vegetative cells' (GO:0009564) mean the formation of a two-celled haploid microgametophyte -- and if so, can it be reworded? And should it have child terms for formation of generative cell and formation of vegetative cell? Jen to check textbooks.
13. Do we need a term for 'protein oxidation'? We have 'lipoprotein oxidation' (GO:0042161), but it's not defined. [Note added during write-up: also have 'protein amino acid oxidation' GO:0018158]
1. Sort out maturation and all children that end in maturation, whether they fit into 'developmental maturation' or 'cell maturation'.
2. Sort out 'cuticle tanning' and parentage.
3. The model definition for reproduction is in GO:0048860. Use this one to formulate all the child definitions.
5. Look at all of the terms that have an is_a relationship to developmental process and group them. Need to create appropriate grouping terms. Come up with Aristotelian definition for the grouping terms.
6. Define root and shoot system development.
7. Check FMA to see how organ and system are defined and related.
8. Ask Eurie to look at whether mating type differentiation child of sex differentiation or not.
9. Check if some single celled stuff falls under multicellular. Use GO term finder and yeast annotations?
10. Differentiate secretion by what is secreted. Leave localization terms as a mixture of cell and organismal processes. Amelia will sort out. Doug also has input. Current placement could be correct.
11. Split transport into cellular and organismal transport. The current transport term is effectively "cellular transport". We've talked about renaming it and adding "organismal transport". Also see SF 1548649 on secretion and transport.
12. Have Doug look at 'cell motility during locomotion' term, definition and placement in graph.
13. Sort out 'locomotion', 'movement', and 'motility'. A gnarly problem indeed.
14. Ask Harold about whether urea cycle metabolism is always organismal metabolism.
15. Check if cell growth has growth and cellular process as parents.
16. Ask Michelle Gwinn about pigmentation. Can we make pigmentation a multicellular organismal process?
COMMENT: (from Michelle via SF item 1562205) Many bacteria certainly produce pigments. There are tons and tons of pigmented bacteria out there in every color of the rainbow. An obvious example are the photosynthetic bacteria. Two examples where some kind of function has been associated with pigment are 1. in Staph the caratenoid pigments appear to play a role in virulence and 2. in Pseudomonase the pigment pyocyanin has a role in iron metabolism (which may also link to virulence). So pigmentation definately happens in proks. - MGG
17. The 'regulation of xxx' terms will need to be dealt with and cleaned up in the future.
18. Since we merged 'physiological process' and 'biological process', we should probably also merge 'regulation of biological process' and 'regulation of physiological process'.
19. Test obomerge (done - Midori)
20. Feature request for obomerge: warn (instead of clobber) if terms in the different changed files share an ID but have different term names, as a way of avoiding ID clashes.
21. Update go/numbers/GO.numbers file (Midori)
22. Assign a separate ID range for each content meeting (Midori; David as backup)
23. Make part_of children of cell cycle is_a cell cycle process (some done at meeting)
24. Add children to 'protein complex assembly', e.g. RNP assembly
25. Look at children of protein complex assembly to see which can go under cellular protein complex assembly
26. Create grouping terms under anatomical structure development to organize children
27. Ditto for cellular process, other high-level terms that wind up with lots of children
27a. Add 'generation of signal' (is_a cellular process; part_of signaling)
27b. Add 'cytokinetic process'
28. Delete 'physiology' from term names (done for some, but not all, sep. regulation terms)
29. Resolve 'GO:' and 'NOM:' IDs -- make sure 0022400 and 0022401 are merged
30. Remove any dodgy instances of '(de)adenylyl' -- may have to change some back to '(de)adenyl' (Midori)
31. Rename all X metabolism, X biosynthesis, and X catabolism terms to X metabolic process, X biosynthetic process, and X catabolic process, respectively (warn the world first!)
32. Sort out synapse-related processes (e.g. synaptic specificity question below); get Erika to help
33. Add synonyms containing 'assembly' to 'complex formation' terms
34. Improve defs for pattern formation terms (David)
35. Ask Erika to check the relationships and definition for determination of muscle attachment site (GO:0016204)
36. Add assembly and disassembly of [unclear whether we wanted 'macromolecular structure' or 'macromolecular complex']
36a. Add cellular structure assembly
37. Create cross-products between 'cellular structure disassembly' and cellular component terms [presumably can do same for cellular structure assembly ...]
37a. Make sure existing structure assembly & disassembly terms are consistent with cellular component ontology (term names and relationships)
38. Add 'extracellular matrix disassembly'
39. Check 'a process' vs. 'the process' in defs throughout; collection-of-processes term defs should have 'a process'
40. Check DNA topological change (GO:0006265) def and relationship to unwinding (Midori)
41. Ask Becky to check the relationships and definition for epidermal growth factor ligand processing (GO:0007174)
42. Carefully craft email on the subject of development vs. developmental process vs. multicellular organismal development; send to GO list (David)
43. When we add the 'regulates' relationship, run Obol to create 'regulation of process X regulates process X' relationships (Chris + curators)
44. add def of AP site to base-excision terms
45. define intussusceptive angiogenesis in 'regulation of cell adhesion during intussusceptive angiogenesis