GO-CHEBI-Agenda: Difference between revisions
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===GOCHE/CHEBI Misalignments=== | ===GOCHE/CHEBI Misalignments=== | ||
We will make requests on the appropriate SF trackers. We should create a group in ChEBI's tracker for GO requests and a group in GO's tracker for ChEBI. | |||
===Edit nucleotide version of CHEBI as Sanity check=== | ===Edit nucleotide version of CHEBI as Sanity check=== | ||
===Roles=== | ===Roles=== |
Revision as of 12:41, 25 July 2010
Attendees:
Saturday
Background and Introduction
- David - Motivation for GOCHE
- Chris - how the original GOCHE file was created
- David - steps leading up to today
- GOALS: GOCHE = CHEBI, improve GO using CHEBI, improve CHEBI using GO
- Chris - process of how improvements to GO using CHEBI will be done
Discussion Areas
Derivatives
- Discuss clarifying the plural terms in CHEBI, we suspect that the plurals represent what we are calling "X and derivative".
- We need a good definition for derivative to use on the '...and derivative' terms Can you help?
- Does modified amino acid mean essentially 'amino acid derivative', in which case shouldn't it have an is functional parent relationship with amino acid?
- Chemists think in terms of chemical skeletons e.g. anything with a phenol aromatic ring is a phenols.
- Derivatives are entities with common substructures, not necessarily actually derived from one another
- The substructure also has to be the main component of the derivative.
- Derivative isn't a very precisely defined term in chemistry
Action for GO: Change `goche id for bezene and derivative for the chebi id for benzenes (uncurated)
- Can we classify chemicals on the basis of the presence of a substructure, regardless of what the rest of the molecule is?
- Could CHEBI to rename/define benzenoid aromatic compound to benzene-containing compound, then GOCHE term benzene and derivative can be mapped to this term rather than benzenes? - yes
- More generally, GOCHE 'x and derivative' terms should be mapped to the 'x-containing compound' parent term rather than the plural
Action for GO: GO to rename the GOCHE 'x and derivative' terms to be 'x-containing compound' throughout
Action for GO: provide CHEBI with a list of the 'x-containing compound' terms for them to add
Conclusion: GOCHE 'x and derivative' terms should be mapped to the 'x-containing compound' (CHEBI will call these 'x-containing molecular entity) parent term rather than the plural. CHEBI will add/rename to create these terms where necessary. These terms will have a has_part relationship to the containing compound.
Macromolecules
- Discuss the inclusion of small molecules into Chebi. Could we have macromolecule vs. monomer? How can we make the distinction of what biologists call a 'small molecule'. What is the complement of macromolecule?
- Meaning of macromolecule in CHEBI to meaning in GOCHE
Conclusion: keep small molecule only in GO - remove from GOCHE. Ensure all children have an alternative structural path.
- Protein and its children - some of these in CHEBI. Are they due to be removed? In PRO?
- Same for RNAs
- CHEBI have discussed proteins with PRO - all protein subtypes will move to PRO.
- Owner of glycoproteins etc yet to be determined. CHEBI might have a term 'protein-chemical complex
- peptide hormones are just peptides and will live in CHEBI, what is a peptide vs. protein? It is ok if the precursors were encoded by the genome.
Nucleotides, nucleosides etc.
- We merged nucleotide and nucleoside phosphate. These seem to be exact synonyms of one another.
- There are non-naturally occurring nucleoside phosphates that are not nucleotides.
- Action for GO: when CHEBI has fixed arrangement of nucleotide phosphate/nucleotide, need to fix GOCHE accordingly (can we write formal definitions for this problem and use this example for the paper?)
- Purine is not currently is_a purines - is this deliberate or an oversight?
- An oversight - CHEBI will fix
- Hypoxantine - should be a purine base in CHEBI?
Action for GO: Move hypoxanthine up to be a child of 'purine-containing compound' (when we have that term)
- Should we merge pyrimidine with pyrimidine (nucleo)base?
- There is a difference between pyrimidine with pyrimidine (nucleo)base - GOCHE should reflect this
- NADH is_a NAD and NADPH is_a NADP. Seems like isa isn't quite right here?
- Action for GO: GOCHE needs to change NAD to NAD+
- Pyridine nucleotide - this looks by its children like it should be a ribonucleotide - should it have this parent/name?
- Carbohydrates and nucleotides - should nucleotide have functional parent rather than is_a carbohydrate (N-glycosyl has functional parent carbohydrate)?
- CHEBI will reorganize these terms using has_part e.g. nucleoside phosphate has_part nucleoside
- Created axioms for nucleobase and nucleoside terms. Tagged with GOC:carnegie dbxref. Will pass on to CHEBI and they will do their magic.
Amino acids
- Amino acid families - not in CHEBI?
- We have removed from GOCHE
- We need a conjugate base term for 'amino acid'. There may be others. Does CHEBI have a systematic way of checking the conjugate base term is always added?
- Relevant files:
- CHEBI_make_links.txt
- CHEBI_oxoacids_no_conjugate_base.txt
- Action for GO: Generate a list of missing conjugate bases for submission to CHEBI. CHEBI will check if the entry already exists, and if it does make the appropriate is_conjugate_base relationship and if not, add it.
Other
- mancude organic heterobicyclic parent CHEBI:35570 - should this term really have 'parent' on the end?
- 48 terms in CHEBI with 'parent' in name.
- Makes a statement about the role of the representation of the molecule in IUPAC (?)
- GOCHE should not directly link to these terms
- In CHEBI sn-glycerol-3-phosphate is_a glycerol-1-phosphate
- An oddity due to IUPACs numbering system. GOCHE can ignore. (sn = stereospecifically numbered)
- In CHEBI pectin is_a galacturonan. We think this should be petin has_part galacturonan - we've put this in GOCHE
- CHEBI will fix this. This is one of the cases where the plural was changed to a singular, but in this case wasn't quite correct because pectin is a mixture of polysaccharides.
- Is an amide an amine?
- Two types of amide: only one is an amine so no.
- Is 'molybdopterin cofactor' a 'pteridine and derivatives' ?
- 'molybdopterin cofactor' would be an intersection term in CHEBI, of the role and the structure.
- Action for GO: Relate this term to the new CHEBI term that refers to the intersection of the CHEBI role and the CHEBI structure
- sulfur metabolism = metabolism of S (element) OR sulfur containing compounds, therefore, do we change 'sulfur metabolism' to 'sulfur and sulfur compound metabolism' - sounds like GO 'sulfur' = CHEBI 'sulfur' = 'sulfur and derivative' and GO 'sulfur compound' = ChEBI 'organosulfur compound'
- CHEBI will change the name of their existing term sulfur molecular entity to term sulfur-containing molecular entity, and add has_part relationship to sulfur.
- Is glyoxylate an aldehyde or not?
- Yes, but GOCHE won't explicitly make it an aldehyde. It will be inferred in a CHEBI relationship.
- adrenocorticotropin, prolactin, somatostatin - do these belong in CHEBI or somewhere else?
- If CHEBI says they are peptides, they will stay under peptides, if not we will put them under proteins and will fall under PRO's scope.
- Would CHEBI consider adding small molecule as a counterpart to macromolecule (see GO def)?
- CHEBI will not add small molecule. GOCHE terms that were children of this term have other parents that trace to chemical already.
- What is the relationship between sphingoid and sphingolipid? Is it upside-down?
- Probably. Will investigate further and fix in CHEBI, if necessary.
Sunday
GOCHE/CHEBI Misalignments
We will make requests on the appropriate SF trackers. We should create a group in ChEBI's tracker for GO requests and a group in GO's tracker for ChEBI.
Edit nucleotide version of CHEBI as Sanity check
Roles
Definition generation
Future
- ChEBI next steps
- GO next steps
- Procedure for future interactions
- Need to prevent drift
- Create GOCHE-GO xps very soon, will transition to CHEBI