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13rd November, 2007
I have solved problems about almost all child terms of "response to drug" term. The changes are already in the lived file.
I have asked to ChEBI people (Kirill) if it would be possible to have these substance in ChEBI molecular structure ontology.We are waiting for that!
List of substances:
KEGG ID C06918
KEGG ID C06943
KEGG ID C07049
KEGG ID C07408
KEGG ID C07274
KEGG ID C06824
KEGG ID D00394
14th November, 2007
I have a thought: proposal for "drug transport" Try to follow ChEBI structure to move all child terms of "drug transport" out of this node.
- Add a new term: GO:0014076 "chemical substance transport"
- Move "chemical substance transport" as is_a child of "transport" general term
- Add a new term: GO:0014077 "organic substance transport"
- Move "organicl substance transport" as is_a child of "transport" general term
- Move "antibiotic transport" as part_of "response to antibiotic"
- Copy "antibiotic transport" as is_a of "chemical substance transport"
- Move "bicyclomycin transport" as is_a "antibiotic transport"
- Copy response to cycloheximide as is_a child of response to antibiotic
- Move "cycloheximide transport" as is_a "antibiotic transport"
- Move tetracyclin transport is_a GO:0014077 "organic substance transport"
- Move organomercurial transport is_a GO:0014077 "organic substance transport"
- Move nalidixic acid transport is_a child of antibiotic transport
- Move alkane transport as is_a child of organic substance transport
- Move carbonyl cyanide m-chlorophenylhydrazone transport as is_a child of organic substance transport
- Move daunorubicin transport as is_a "antibiotic transport"
To be asked GO curator
- Maybe I need to create a branch file in scratch directory named response_to_drug.obo
- Proposal to obsolete drug export GO:0046618 has just 12 gene associations
- Proposal to merge multidrug transport GO:0006855 .It has almost the same defintion of drug transport GO:00415893 but it has 318 gene associations.So we could merge it with "chemical substance transport"
To be asked ChEBI curator
15th November, 2007
This is my work on "response to drug" so far. picture of response to drug work
16th November, 2007
New compounds have been added into ChEBI. Thisi s the list:
methotrexate (CHEBI:44185) is a pteridines (CHEBI:26373)
Tricyclic antidepressants: clomipramine (CHEBI:47780) desipramine (CHEBI:47781) imipramine (CHEBI:47499) lofepramine (CHEBI:47782) nortriptyline (CHEBI:7640) protriptyline (CHEBI:8597) trimipramine (CHEBI:9738)
I move methotrexate out of "response ot drug"
17th, December, 2007
I addded response to fluoxetine GO:0014076 has chil of Organic cyclic substance