gocentral
commented
18 years ago Original comment by: addiehl
Closed gocentral closed 9 years ago
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=865072
Also, and most importantly, I thank Jamie Lee in particular for her work on various parts of the ontolgoy, and the participants in the GO Content Meeting last November for their invaluable help as well.
-- Alex
Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=451873
Hi Alex - would it be possible for you to post the master file for people who are a bit more au fait with using OBO-Edit? I'd like to see the full parentage for the new terms. cheers, jane.
Original comment by: jl242
gocentral
commented
18 years ago Logged In: YES user_id=473796
Hi Alex,
Here are my comments:
- I've uploaded a new version of the file in which I've made a number of changes
-- term names with strange capitalization, punctuation -- typos / double spaces, etc., in term defs -- terms with is-a and part-of relationships to the same parent -- organisms referred to as plurals (e.g. fungi) changed to singular (e.g. fungus) -- removed articles from term names except for the "in the context of an immune response" terms - see below for more on those -- "in" changed to "during" in terms where "in" was temporal
* "antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II"
* "antigen processing and presentation, lipid antigen" and "antigen processing and presentation, polysaccharide antigen" don't exist, but logically it seems that they should. If lipid antigen p&p and polysacch antigen p&p only ever occur via MHC class Ib and MHC class II respectively, we could add those term strings as exact synonyms of the existing terms.
* "lipid antigen transport" is currently part of lipid antigen p&p - does lipid antigen only ever occur as part of this process or might it occur at other times? This term could also have parentage under transport in the main ontology.
* "peptide assembly with MHC protein complex"
* GO:0002492 has the name "peptide antigen assembly with MHC class Ib protein complex", whereas its siblings and parents are named "peptide assembly with MHC ... protein complex". I presume that this is deliberate?
* we should really have generic parents for "polysaccharide assembly with MHC class II protein complex" and "lipid antigen assembly with MHC class Ib protein complex" - if you don't want to make terms like "lipid antigen assembly with MHC protein complex", we can have a more generic term like "lipid antigen binding during protein complex assembly".
* "proteolysis associated with antigen processing and presentation" and children - the defs for these terms read "The hydrolysis of a peptide bond or bonds within a protein during antigen processing and presentation." - is there any reason why the terms read "associated with" rather than "during"? I have changed them in the uploaded file.
* "in the context of an immune response" - I don't like this string very much. There seem to be two sets of terms with this string in them; one set where the def specifies it happens during the immune response, and the other where the def says "leading to the initiation or perpetuation of an immune response.". The first set could be renamed "xxx during immune response" and I've done so in the new version of the file. Perhaps the second set could be renamed "immune response-related xxx", e.g. "immune response-related endothelial cell activation within high endothelial venule"? "In the context of" sounds wrong to me. :\
* "cytokine production in acute inflammatory response" et al. - the def says "during", so I have changed the term string to match the standard GO nomenclature
* "platelet activating factor production during acute inflammation ; GO: 0002391" - the child is named "platelet activating factor secretion during acute inflammatory response ; GO:0002535". Should GO:0002391 be renamed "... during acute inflammatory response" and should inflammatory response terms have inflammation synonyms?
* "activation of immune response" should be a child of "positive regulation of immune response", rather than "immune response" - have moved it
I haven't really looked at all the parentage fully - I'd like to see the full tree that Jane mentions below.
Great work Alex, Jamie and everyone else!
Original comment by: girlwithglasses
gocentral
commented
18 years ago Original comment by: girlwithglasses
gocentral
commented
18 years ago Logged In: YES user_id=473796
Adding file with typos corrected.
Original comment by: girlwithglasses
gocentral
commented
18 years ago Logged In: YES user_id=473796
PAMGO would like a term to encompass the production (vs the biosynthesis) of phytoalexins as part of the defense response. In this proposal, we've got 'induction of phytoalexin biosynthesis' as a child of 'activation of innate immune response (sensu Viridi...)'; if we added some new terms as follows, can you suggest how they would be linked into the immunology terms?
phytoalexin production [p] phytoalexin biosynthesis [p] phytoalexin secretion [p] regulation of phytoalexin production ---[i] induction of phytoalexin production <-- term wanted by PAMGO
Thanks, Amelia.
Original comment by: girlwithglasses
gocentral
commented
18 years ago Logged In: YES user_id=865072
Amelia and Others,
I am preparing a revised version of the file incorporating many of the suggested changes and will include the phytoalexin terms. I will post the file later in the week.
-- Alex
Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=473796
Thanks Alex!
I'm working on PAMGO stuff at the moment which intersects with the immune response terms, so I hope you don't mind if I keep on posting questions or comments here.
Reactive oxygen species: You have nitric oxide down as a reactive oxygen species, but elsewhere in the GO, we've got the ROSs defined as "...singlet oxygen, superoxide, and oxygen free radicals" (GO:0000302; see also GO:0006800), and nitric oxide isn't classed as one. PAMGO have proposed a term to represent evasion or tolerance by organism of host-produced nitric oxide, which is separate from evasion or tolerance by organism of host oxidative burst (production of ROSs by the host). Can we make uniform how we refer to NO? I would suggest separating it from ROSs since that's how it is represented in most of the ontology.
Original comment by: girlwithglasses
gocentral
commented
18 years ago Logged In: YES user_id=473796
Oxidative burst: PAMGO would like a term to describe the response of the symbiont to a host oxidative burst (as part of the host defense response).
There's a general def of oxidative burst at wikipedia: http://en.wikipedia.org/ wiki/Oxidative_burst or just google for it.
How does your term 'production of reactive oxygen species during acute inflammatory response ; GO:0002536' correspond to defense-related oxidative burst? Are they the same or is GO:0002536 more specific? If so, we would like to add a new term for oxidative burst during defense response.
Original comment by: girlwithglasses
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=865072
Amelia,
I've altered the term name definition of GO:0002536 to model it more after the generic definition provided for respiratory burst ; GO:0045730 and to delete the reference to nitric oxide. I also made production of nitric oxide during acute inflammatory response ; GO:0002537 a direct is_a to production of molecular mediators of inflammatory response; GO:0002532, rather than to GO:0002536.
In GO and Wikipedia, 'respiratory burst' is used instead of oxidative burst, as essentially an exact synonym, which I agree is okay based on the primary biomedical literature. 'Respiratory burst' is slightly more common than 'oxidative burst' in PubMed. We need to have "oxidative burst" as a synonym for the existing GO "respiratory burst" terms.
Clearly "respiratory burst during defense response" is a more general term than "respiratory burst during acute inflammatory response," as both plants and animals use such a process as part of innate immune responses, but only vertebrates have inflammatory responses.
Thus we have:
respiratory burst ; GO:0045730 --% respiratory burst during defense response ; GO:0002679 ----% respiratory burst during acute inflammatory response ; GO:0002536 ----% respiratory burst after phagocytosis ; GO:0045728
physiological defense response ; GO:0002217 --% innate immune response ; GO:0045087 ----% respiratory burst during defense response ; GO:0002679 ------% respiratory burst during acute inflammatory response ; GO:0002536 ------% respiratory burst after phagocytosis ; GO:0045728
immune effector process ; GO:0002252 --% respiratory burst during defense response ; GO:0002679 ----% respiratory burst during acute inflammatory response ; GO:0002536 ----% respiratory burst after phagocytosis ; GO:0045728
production of molecular mediators of inflammatory response; GO:0002532 --% respiratory burst during acute inflammatory response ; GO:0002536 --% production of nitric oxide during acute inflammatory response ; GO: 0002537
I'm uploading a pdf of a graphical view of this set of terms as well.
-- Alex
Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=473796
Hi Alex,
Thanks for all the changes! Would it be possible to see the whole of the process ontology with the immunology proposal in place?
Thanks, Amelia.
Original comment by: girlwithglasses
gocentral
commented
18 years ago Logged In: YES user_id=865072
Amelia,
I am very close to producing that, but will be on vacation from today until Tuesday next week, so I will send it out probably one week from today. Sorry for the delay, but we are nearly there.
-- Alex
Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=473796
I couldn't see anything in the file on this but it may be elsewhere; are there to be any terms covering defense-related calcium ion fluxes?
Original comment by: girlwithglasses
gocentral
commented
18 years ago Logged In: YES user_id=473796
And also any defense-related calcium-dependent protein kinase signalling pathways?
Original comment by: girlwithglasses
gocentral
commented
18 years ago Logged In: YES user_id=473796
And another one - MAPK signalling pathways as part of the defense response?
Original comment by: girlwithglasses
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=865072
Final Version, Immunology Revision
The revision includes 619 new terms and changes to many existing terms, in term names, definitions, and/or linkages. Two terms are being obsoleted and 26 terms merged with other terms, as described below. The new terms have IDs in the range GO:0002200-GO:0002818.
I've uploaded both the separate ontology for the immunology revision (immunologyR5.obo.zip) and the revised form of the GO biological_process ontology incorporating the revision, which is broken into four zipped files that have to be rejoined using a text editor (so primitive, but SourceForge made me do it) before being loaded into OBO-Edit. I can email the whole file (gene_ontology_BP_immunology.obo.zip) upon request. In any case, I invite people to look these files over. As far as the final implementation of the revision, we could do it here at MGI or the EBI people can do it if they have a good tool for merging the ontologies. Let me know.
Features of the Immunology Revision All of the non-regulation terms include is_a parents; I've added some of the missing parents even for the existing terms. Many of the "regulation of X" terms lack is_a parents, and in fact I broke down much of the existing regulation term hierarchy, so that OBOL can be used to rebuild it to match the new structure in the ontology. In all cases "regulation of X" terms are part_ofs to the "X" process terms, so OBOL will have a structure to follow.
Most of the non-regulation terms have actual literature references, sometimes multiple ones. I have spent enormous time and effort developing these terms and finding good references for them.
I've added huge number of synonyms, most trivial ones (B cell, B-cell etc.).
I thank Jamie Lee for her many term contributions, and Jamie and Richard Scheuermann for their excellent comments and suggestions on the penultimate form of the revision and additional terms.
I thank Amelia Ireland too for her many suggestions, which I will address here:
I included her many fixes to spelling, capitalization etc., and fixed many additional ones. I changed all organisms to singular forms per her suggestion. I changed all "in" to "during" and "in the context of immune response" to "during immune response" per her suggestions.
I've kept my formulation of the antigen processing and presentation term names, although I did systematize them a bit more and got rid of parentheses in certain names (these existed already in the GO, I didn't start their use). I prefer my formulation of the names, and since I wrote them, I would like them to remain as they are written. Given that Jamie and Richard did not have any problems with these names, I think they are fine.
I kept "proteolysis associated with antigen processing and presentation" instead of "proteolysis during antigen processing and presentation," in parent term and children. I also rephrased the definition to remove the word "during." The use of the word "during" implies such proteolysis is somehow exclusively part of the process of APP when in fact proteolysis of all kinds occurs during cellular life. Some proteolytic systems adventitiously yield peptides that are capable of binding MHC molecules, but these systems, such as the proteosome or endosomal or lysosomal proteases, are turned on continuously for purposes of general protein catabolism as part of cellular homeostasis. APP, too, is turned on continuously, and the two processes are sometimes coregulated, but the proteolysis is not exclusively part of APP.
I made "activation of immune response" a child of "positive regulation of immune response" per Amelia suggestion. Good suggestion.
I kept "tolerance induction dependent upon immune response," over "immune response-dependent tolerance induction," which I felt was an entirely arbitrary rephrasing of the original which I did not prefer. I did add the rephrasing as an exact synonym.
I kept the names of the various T cell subtypes as they are written in the Cell Ontology (which is a base ontology for the GO), using, for instance "CD4- positive, alpha-beta T cell" instead of "CD4-positive alpha-beta T cell."
For the sake of time, I decided to leave out the phytoalexin production, secretion, and biosynthesis terms. I did reform and expand the antimicrobial peptide terms, and I think the phytoalexin terms can be easily added to the structure.
I followed Amelia's advice regarding the reactive oxygen terms.
I haven't added anything relating to "defense-related calcium fluxes" or "defense related calcium-dependent protein kinase signaling pathways" or "defense-related MAPK signaling pathways." It's not entirely clear to me why we need to enumerate these very basic types of signaling pathways which are involved in all kinds of cell signaling including that which occurs as part of immune or defense responses as separate cross-products of "defense response" and particular signaling pathways, when coannotation is sufficient to indicate the connection for particular gene products. In any case, I would need to study the issue more to decide the best approach and will leave the problem to others for the moment if there is some urgency.
Terms being obsoleted
GO:0006969, melanotic tumor response This term is undefined and unused, and based on Pubmed abstracts appears to refer to tumor treatment regimens, not a normal biological process.
GO:0016065, humoral defense mechanism (sensu Protostomia) This term refers to antibodies in the taxon Protostomia, which simply do not exist. Insects and other Prostomites have other types of immune receptors, but not antibodies. There are 7 NAS annotations to this term directly, from Flybase, based on sequence records. I'm not sure what information was intended to be captured by these annotations, but perhaps the records should be recurated.
Terms being merged Most terms that were merged are the "pathogen" terms that were discussed at great length and people (including PAMGO) agreed to eliminate for reasons I don't really want to rehash here.
GO:0009613, response to pest, pathogen or parasite GO:0042828, response to pathogen These terms are being merged with GO:0051707, response to other organism because responses to organism considered by humans to be pathogens, pests, and parasites occur in the same manner as responses to other organisms in general. It is better to annotate to organism-specific terms, particular symbiosis terms, and/or particular defense response terms.
GO:0009596, detection of pest, pathogen or parasite This term is being merged with their parent term GO:0009595, detection of biotic stimulus, for similar reasons as above.
GO:0009681, detection of non-pathogenic bacteria GO:0009598, detection of pathogenic bacteria These terms are being merged with their parent term GO:0016045, detection of bacterium (slight name change for GO:0016045 as well), as the means of detecting bacteria are the same irregardless of the eventual outcome of the interaction with the bacteria.
GO:0009680, response to non-pathogenic bacteria GO:0009618, response to pathogenic bacteria These terms are being merged with their parent term GO:0009617, response to bacterium (slight name change for GO:0009617 as well), as responses to bacteria occur without prior knowledge of the outcome of the interaction.
GO:0042830, defense response to pathogenic bacteria This term is being merged with its parent term GO:0042742, defense response to bacterium (slight name change for GO:0042742), because defense responses to bacteria occur without prior knowledge of the outcome of the interaction.
GO:0009599, detection of pathogenic fungi This term is being merged with its parent GO:0016046, detection of fungus (slight name change for GO:0016046) as the means of detecting fungi are the same irregardless of the eventual outcome of the interaction with the fungi.
GO:0009621, response to pathogenic fungi This term is being merged with its parent term GO:0009620, response to fungus (slight name change for GO:0009621), as responses to fungi occur without prior knowledge of the outcome of the interaction.
GO:0042831, defense response to pathogenic fungi This term is being merged with its parent term GO:0050832, defense response to fungus (slight name change for GO:0042831), because defense responses to fungi occur without prior knowledge of the outcome of the interaction.
GO:0042833, response to pathogenic protozoa This term is being merged with its parent term GO:0001562, response to protozoan (slight name change for GO:0001562), as responses to protozoa occur without prior knowledge of the outcome of the interaction.
GO:0042829, defense response to pathogen This term is being merged with the new term GO:0002217, physiological defense response, since when defense response occur, they occur without prior knowledge of the outcome of the interaction, since many bacteria, fungi, protozoa etc., are pathogenic only in particular situations, but are responded to as potential pathogens whether or not they are capable of causing disease.
GO:0043019, response to pathogenic insect This term is being merged with GO:0009625, response to insect, as responses to insects occur without prior knowledge of the outcome of the interaction.
GO:0042154, attenuation of antimicrobial humoral response (sensu Protostomia) GO:0042155, attenuation of antimicrobial humoral response (sensu Vertebrata) Both terms are being merged with their parent term GO:0008348, attenuation of antimicrobial humoral response
GO:0016066, cellular defense response (sensu Vertebrata) GO:0016067, cellular defense response (sensu Protostomia) These terms are being merged with their parent term, GO:0006968, cellular defense response, whose definition is unchanged, but which now has a comment indicated that the term covers any type of defense response mediated by a cell, whether a single-celled organism or part of a multicellular organism. GO:0016066 has never been used, and GO:0016067 has been used primarily for genes involved in the immune response, which are not necessarily incorrect annotations, but hopefully now with many more specific terms available, better terms will be chosen instead of or in addition to this term.
GO:0042087, cell-mediated immune response This term is being merged with the new term GO:0002443, leukocyte mediated immunity. Immunologists have often used the phrase cell- mediated immune response to indicate immune responses involving T cells, but the existing definition of GO:0042087 does not mention T cells. Merging the term to the new term should clarify the meaning and preserve all annotations as being correct whether they referred to T cells or leukocytes in general.
GO:0045845, regulation of natural killer cell activity GO:0030102, negative regulation of natural killer cell activity GO:0045846, positive regulation of natural killer cell activity These three terms are being merged, respectively, with GO:0002715, regulation of natural killer cell mediated immunity, GO:0002716, negative regulation of natural killer cell mediated immunity, and GO:0002717, positive regulation of natural killer cell mediated immunity. The original terms lacked a proper parent "natural killer cell activity," and the meaning of activity was vague. The new terms fit the overall paradigm of X cell immunity, with specific types of effecter processes enumerated as children. The existing annotations (5) appear to be valid for the new terms.
-- Alex
Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=451873
Alex - we usually do this sort of large-scale merge using the Mac text editor BBEdit, which has a really useful compare files feature (it's more or less impossible to do using cvs).
It's going to be a bit of a big job doing this, and I'm afraid I don't really have time to commit to doing it just at the moment, especially if we want to get this in before the advisory board meeting (I don't know if any of the other EBI people has time?). But if you or Harold has BBEdit (or something similar), I'd be happy to guide you through the process.
jane
Original comment by: jl242
gocentral
commented
18 years ago Logged In: YES user_id=473796
I can commit this when I add the PAMGO terms, as I have been loading and referring to the immunology revision whilst I've been working through the PAMGO stuff, and there are some areas of overlap between the two. I haven't yet had a look through this revision, though, and I don't know if there are going to be any issues with the PAMGO proposals.
Amelia.
Original comment by: girlwithglasses
gocentral
commented
18 years ago Logged In: YES user_id=865072
Jane and Amelia,
I don't mind if this is put off for a week, although I know that Judy was
anxious to have this implemented in time for the GO Advisory Board Meeting.
I do have a perl script to merge ontology files, which is how I did the merge
of the subontology to the BP ontology. I also have BBEdit 7.1.4 and
Textwrangler 2.1.3 (the free, striped-down version of BBEdit that does most
of the same things), so I'd be happy to have a go at following your
instructions or using my own script.
I did discover one missing link yesterday, as well as 13 additional terms for which I would like to create regulation terms. Perhaps I will add those terms in -- I don't think it will affect Amelia's review of the file too significantly, and I can send you both the updated version if you like, as well as place the updated the files here.
I haven't really looked carefully at the PAMGO terms yet, but will try to today.
-- Alex
Original comment by: addiehl
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=865072
I took advantage of the pause caused by Jane's absence at the GO advisory board meeting to make some corrections and add some regulation terms I missed before in the Immunology revision.
I've now uploaded a set of files that represent a corrected and expanded version of the Immunology Revision. These files all end in R6 and include the revision as a subontology (immunologyR6.obo.zip) and four files that contain the whole GO biological_process ontology with the immunology revision folded in. These four files must be unzipped and joined with a text editor before being loaded into OBO-Edit. I can send a single file with the GO BP to anyone by email upon request.
A small number of linkage errors have now been corrected, and a small number of non-regulation terms have been added, mostly terms that got "misplaced" in the process of developing the revision which I have now recovered. I also added another whole lot of regulation terms, so that now the new term count is at 726 new terms between GO:0002200 and GO:
Comments and additional corrections are always welcome, but otherwise I would like to get this implemented as soon as possible.
-- Alex
Original comment by: addiehl
gocentral
commented
18 years ago Logged In: YES user_id=451873
Don't wait for me - Amelia, can you just add these asap do you think? Just get it committed, we can fix minor stuff after it's in...
thanks!
jane
Original comment by: jl242
gocentral
commented
17 years ago Logged In: YES user_id=865072
The immunology revision is now committed.
Thanks to all for your help.
-- Alex
Original comment by: addiehl
gocentral
commented
17 years ago Original comment by: addiehl
gocentral
commented
17 years ago Original comment by: mah11
I am submitting an obo formatted file of the revision of the immunology and response and detection terms (file is zipped). This is close to the final form of the revision, and I invite all interested parties to browse the file using OBO-Edit for its scientific content and ontological structure and submit comments to me either through this SourceForge entry or directly by email (adiehl@informatics.jax.org).
Please note that this is only a sub-ontology of the biological_process ontology and I have left out the "dangling links" to prevent confusion for people less familiar with OBO-Edit. The links to other terms in the biological_process ontology are present in the master file which will be used to modify the gene_ontology.obo file when the time comes.
Also a few terms appear unrooted, but again, this is only because this is a sub-ontology of the biological_process ontology. Also, some is_a parents are not present in this sub-ontology but will exist once the sub-ontology is merged with the whole biological process ontology.
A number of standard synonyms are still missing for some of the terms, such as T cell, T-cell, T lymphocyte, T-lymphocyte, but I will add these shortly. I have included many regulation terms, but may create more as well before the final implementation. Note that the existing regulation term hierarchies have been "broken down" and will have to be rebuilt with OBOL to reflect the updated structure.
The new terms are between GO:0002200 and ~GO:0002700. I have also modified many existing term names and definitions. There will be some obsoletions as well, particularly for certain "pathogenic" terms, but these are not included in this file at this time.
I have included several new terms related to tumor immunology as well.
I will be on vacation until July 31 after today, and look forward to your comments on my return. I will wait three weeks total for comments, prior to implementation.
Thanks,
Alex
Reported by: addiehl
Original Ticket: "geneontology/ontology-requests/3462":https://sourceforge.net/p/geneontology/ontology-requests/3462