Difference between revisions of "Implementation"

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== 13rd November, 2007 ==
 
== 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.<br>
 
I have solved problems about almost all child terms of "response to drug" term. The changes are already in the lived file.<br>
 +
 +
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<br>
 +
CHEBI:44185 unclassified<br>
 +
 +
CLOMIPRAMINE<br>
 +
tricyclic antidepressant<br>
 +
KEGG ID C06918<br>
 +
CAS    303-49-1<br>
 +
 +
DESIPRAMINE<br>
 +
tricyclic antidepressant<br>
 +
KEGG ID C06943<br>
 +
CAS    50-47-5<br>
 +
 +
IMIPRAMINE<br>
 +
tricyclic antidepressant<br>
 +
KEGG ID C07049<br>
 +
CAS    50-49-7<br>
 +
 +
LOFEPRAMINE<br>
 +
tricyclic antidepressant<br>
 +
KEGG ID C07408<br>
 +
CAS    438-60-8<br>
 +
 +
NORTRIPTYLINE<br>
 +
tricyclic antidepressant<br>
 +
KEGG ID C07274<br>
 +
CAS    72-69-5<br>
 +
 +
PROTRIPTYLINE
 +
tricyclic antidepressant<br>
 +
KEGG ID C06824<br>
 +
CAS    50-48-6<br>
 +
 +
TRIMIPRAMINE<br>
 +
tricyclic antidepressant<br>
 +
KEGG ID D00394<br>
 +
CAS    739-71-9<br>
 +
  
 
== 14th November, 2007 ==
 
== 14th November, 2007 ==
Make a branch file in go/scratch directory named response_to_drug.obo
 
  
format-version: 1.2
+
'''I have a thought: proposal for "drug transport"'''
date: 13:11:2007 17:31
+
Try to follow ChEBI structure to move all child terms of "drug transport" out of this node.
saved-by: erika
 
auto-generated-by: OBO-Edit 1.101
 
subsetdef: goslim_candida "Candida GO slim"
 
subsetdef: goslim_generic "Generic GO slim"
 
subsetdef: goslim_goa "GOA and proteome slim"
 
subsetdef: goslim_pir "PIR GO slim"
 
subsetdef: goslim_plant "Plant GO slim"
 
subsetdef: goslim_yeast "Yeast GO slim"
 
subsetdef: gosubset_prok "Prokaryotic GO subset"
 
default-namespace: gene_ontology
 
remark: cvs version: $Revision: 5.544 $
 
  
I am working on "drug transport" term.<br>
 
 
*Add a new term: GO:0014076 "chemical substance transport"<br>
 
*Add a new term: GO:0014076 "chemical substance transport"<br>
 
*Move "chemical substance transport" as is_a child of "transport" general term<br>
 
*Move "chemical substance transport" as is_a child of "transport" general term<br>
Line 37: Line 67:
  
 
'''To be asked GO curator'''
 
'''To be asked GO curator'''
*I need to create a branch file in scratch directory named response_to_drug.obo
+
*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 6 gene associations
+
*Proposal to obsolete drug export GO:0046618 has just 12 gene associations
*Proposal to obsolete multidrug transport GO:0006855 .It has almost the same defintion of drug transport GO:00415893 but it has 318 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'''
+
'''To be asked ChEBI curator''' WAIT before doing that!!!!<br>
 
*amiloride
 
*amiloride
 
*acriflavine
 
*acriflavine

Revision as of 01:10, 15 November 2007

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


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 WAIT before doing that!!!!

  • amiloride
  • acriflavine
  • azole
  • benomyl
  • cycloheximide