Implementation

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[edit] 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:

METHOTREXATE
CHEBI:44185 unclassified

CLOMIPRAMINE
tricyclic antidepressant
KEGG ID C06918
CAS 303-49-1

DESIPRAMINE
tricyclic antidepressant
KEGG ID C06943
CAS 50-47-5

IMIPRAMINE
tricyclic antidepressant
KEGG ID C07049
CAS 50-49-7

LOFEPRAMINE
tricyclic antidepressant
KEGG ID C07408
CAS 438-60-8

NORTRIPTYLINE
tricyclic antidepressant
KEGG ID C07274
CAS 72-69-5

PROTRIPTYLINE tricyclic antidepressant
KEGG ID C06824
CAS 50-48-6

TRIMIPRAMINE
tricyclic antidepressant
KEGG ID D00394
CAS 739-71-9


[edit] 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

  • amiloride
  • acriflavine
  • azole
  • benomyl
  • cycloheximide

[edit] 15th November, 2007

This is my work on "response to drug" so far. picture of response to drug work

[edit] 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"

[edit] 17th, December, 2007

I added response to fluoxetine GO:0014076 has child of organic cyclic substance

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