Isa-complete BP

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Notes on making the biological process ontology is_a complete

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.

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.

Multi-organism: accepted

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 partially implemented in the working draft)

1. 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

2. ‘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

3. May want to make a term 'cell division of a single celled organism' and make that a synonym of cellular reproduction.

4. May want 'multicellular organismal sex determination' and 'single cell sex determination' for grouping. Possibly also 'multicellular organismal sex development'.

5 . 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.

Open Questions

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

2. Do we need regulatory process in addition to regulation?

3 Do we need a higher level term: cell population process?

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?

5. Should intracellular signaling cascade, or its parent signal transduction, be is_a cellular physiological process? See SF 1558514.

To do list

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?

17. The 'regulation of xxx' terms will need to be dealt with and cleaned up in the future.