Difference between revisions of "Implementation"

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#REDIRECT [[Defunct]]
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[[Category:Ontology]]
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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
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'''I have a thought: proposal for "drug transport"'''
date: 13:11:2007 17:31
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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 70:
  
 
'''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
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*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.
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*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'''
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'''To be asked ChEBI curator'''<br>
 
*amiloride
 
*amiloride
 
*acriflavine
 
*acriflavine
Line 47: Line 80:
 
*benomyl
 
*benomyl
 
*cycloheximide
 
*cycloheximide
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== 15th November, 2007 ==
 +
 +
This is my work on "response to drug" so far.
 +
[http://gocwiki.geneontology.org/index.php/Image:Response_to_drug.png 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 added response to fluoxetine GO:0014076 has child of organic cyclic substance

Latest revision as of 15:25, 6 March 2020

Redirect to:


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

  • amiloride
  • acriflavine
  • azole
  • benomyl
  • cycloheximide

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