Difference between revisions of "Implementation"

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(New page: == CASE OF "RESPONSE TO ORGANIC SUBSTANCE" GO: 0010033 == In the ChEBI ontology there is "organic molecular compound" CHEBI:25700, defined as a molecular entity that contain carbon and ...)
 
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== CASE OF "RESPONSE TO ORGANIC SUBSTANCE" GO: 0010033 ==
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== 13rd November, 2007 ==
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I have solved problems about almost all child terms of "response to drug" term. The changes are already in the lived file.<br>
  
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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!
  
In the ChEBI ontology there is "organic molecular compound" CHEBI:25700, defined as a molecular entity that contain carbon and its synonyms are: organic compounds and organic entity. In the GO the definition of "response to organic substance" GO:0010033 term is: a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. But, what do we mean for "organic substance"? We can use the definition of ChEBI:25700 for defining what is an organic substance.
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List of substances:
After that, we can use the "response to organic substance" GO:0010033 as a parent term and moving many terms from "resposne to drug" under this term: see the case of cycloheximidine GO:0046898
 
  
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METHOTREXATE<br>
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CHEBI:44185 unclassified<br>
  
When I start to use the ChEBi ontology as a reference to insert new terms in the GO, I relised that I have three cases:<br>
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CLOMIPRAMINE<br>
1. the compound in which I am interested is present in the ChEBI molecular structure ontology (example morphine)<br>
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tricyclic antidepressant<br>
Solution: I will stick part or all the ChEBI structure in the GO<br>
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KEGG ID C06918<br>
2. my compound is not included in the ChEBI molecular structure ontology but it is present in the other ChEBI ontology (application and molecular role) (example: amphetamine)<br>
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CAS    303-49-1<br>
Solution: First, I will request to ChEBI curators to have the term amphetamine under molecular structure ontology and then I will add a new term in the GO<br>
 
3. my compound is not included in the ChEBI ontology (example Citalopram) or it is a preliminary entry (example fluoxetine ChEBI 5118)<br>
 
Solution: I will request a new term to ChEBI people
 
<br>
 
  
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DESIPRAMINE<br>
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tricyclic antidepressant<br>
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KEGG ID C06943<br>
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CAS    50-47-5<br>
  
== 1) CASE OF CYCLOHEXIMIDE GO:0046898 ==
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IMIPRAMINE<br>
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tricyclic antidepressant<br>
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KEGG ID C07049<br>
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CAS    50-49-7<br>
  
Cycloximide is a child of resposne to antibiotic (GO:00) but we would like to classify this substance not following its role in the cell but on the base of its moleculare strucuture.
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LOFEPRAMINE<br>
So, looking in the ChEBI ontology, we can find that it is a child of cycloalkanes (Fig.1).
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tricyclic antidepressant<br>
Using the ChEBI structure, we could implement it in the GO moving the term "response to Cycloheximide" GO 0046898 at the end we have the DAG structure showed in the Fig.1.
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KEGG ID C07408<br>
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CAS    438-60-8<br>
  
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NORTRIPTYLINE<br>
Figure 1
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tricyclic antidepressant<br>
[[http://gocwiki.geneontology.org/index.php/Image:Picture_6.png]]
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KEGG ID C07274<br>
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CAS    72-69-5<br>
  
We could do the same for response to bacteriocin GO:0046678, response to brefeldin A GO:0031001 and response to streptomycin GO:0046679.
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PROTRIPTYLINE
For streptomycin it would be easy because it is already present in ChEBI ontology (CHEBI:17076); instead for the others we should request new terms to ChEBI curators and wait until they implement them into the ontology.
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tricyclic antidepressant<br>
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KEGG ID C06824<br>
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CAS    50-48-6<br>
  
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TRIMIPRAMINE<br>
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tricyclic antidepressant<br>
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KEGG ID D00394<br>
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CAS    739-71-9<br>
  
  
== 2) CASE OF MORPHINE GO:0043278 ==
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== 14th November, 2007 ==
  
"response to morphine" GO:0043278 is an other term having a correspondent one in the ChEBI ontology CHEBI:17303 morphine.
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'''I have a thought: proposal for "drug transport"'''
The Fig.2 shows the final structure of GO DAG after the implementation of some new terms like "response to isoquinoline alkaloid".
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Try to follow ChEBI structure to move all child terms of "drug transport" out of this node.
  
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*Add a new term: GO:0014076 "chemical substance transport"<br>
Figure 2
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*Move "chemical substance transport" as is_a child of "transport" general term<br>
[[http://gocwiki.geneontology.org/index.php/Image:Picture_7.png]]
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*Add a new term: GO:0014077 "organic substance transport"<br>
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*Move "organicl substance transport" as is_a child of "transport" general term<br>
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*Move "antibiotic transport" as part_of "response to antibiotic"
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*Copy "antibiotic transport" as is_a of "chemical substance transport"<br>
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*Move "bicyclomycin transport" as is_a "antibiotic transport"<br>
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*Copy response to cycloheximide as is_a child of response to antibiotic<br>
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*Move "cycloheximide transport" as is_a "antibiotic transport"<br>
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*Move tetracyclin transport is_a GO:0014077 "organic substance transport"<br>
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*Move organomercurial transport is_a GO:0014077 "organic substance transport"<br>
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*Move nalidixic acid transport is_a child of antibiotic transport<br>
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*Move alkane transport as is_a child of organic substance transport<br>
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*Move carbonyl cyanide m-chlorophenylhydrazone transport as is_a child of organic substance transport<br>
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*Move daunorubicin transport as is_a "antibiotic transport"<br>
  
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'''To be asked GO curator'''
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*Maybe I need to create a branch file in scratch directory named response_to_drug.obo
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*Proposal to obsolete drug export GO:0046618 has just 12 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"
  
== 3) CASE OF FLUOXETINE GO:null CHEBI: 5118 ==
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'''To be asked ChEBI curator'''<br>
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*amiloride
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*acriflavine
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*azole
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*benomyl
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*cycloheximide
  
There are many terms of interest to pharmaceutical researchers for the annotation of gene products that responde to the administration of a specific drug, for instance "response to fluoxetine". Fluoxetine is an antidepressant, in detail it is a selective serotonin reuptake inhibitors (SSRIs) which is derived from diphenhydramine, an antihistamine found to inhibit reuptake of the neurotransmitter serotonin (Fig.3)
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== 15th November, 2007 ==
  
The list of antidepressants is very long and I have start to request new terrms to CHEBI curators with the aim to add these ones in the GO.
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This is my work on "response to drug" so far.
In the next CHEBI release, we should have these new terms:
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[http://gocwiki.geneontology.org/index.php/Image:Response_to_drug.png picture of response to drug work]
SERTRALINE
 
PAROXETINE
 
CITALOPRAM
 
VENLAFAXINE
 
ESCITALOPRAM
 
FLUVOXAMINE
 
BUPROPION
 
DULOXETINE
 
AMITRIPTYLINE
 
DOTHIEPIN
 
  
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== 16th November, 2007 ==
Figure 3
 
[[http://gocwiki.geneontology.org/index.php/Image:Picture_5.png#filelinks]]
 
  
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New compounds have been added into ChEBI.
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Thisi s the list:
  
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methotrexate (CHEBI:44185) is a pteridines (CHEBI:26373)
  
Some Questions and Some Answers:
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Tricyclic antidepressants:
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clomipramine (CHEBI:47780)
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desipramine (CHEBI:47781)
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imipramine (CHEBI:47499)
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lofepramine (CHEBI:47782)
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nortriptyline (CHEBI:7640)
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protriptyline (CHEBI:8597)
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trimipramine (CHEBI:9738)
  
1) Do we need to stick all the ChEBi structure or can we choose only the terms that we need for classify our GO "response to X" term?<br>
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I move methotrexate out of "response ot drug"
We decided to choose only the terms that we need for insert our "response to X" term in a correct structure<br>
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2) Have innumerable children under response to chemical parent term is not a problem. Is it true?<br>
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== 17th, December, 2007 ==
Yes, it is true. We can have as many children as we need.<br>
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3) we want to use synonym for better describing the term. For example, "response to fluoxetine" could have a related synonym "response to antidepressant" or a more informative one "response to selective serotonin reuptake inhibitors".Doing that, we could have additional information about the use of a substance as a drug.<br>
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I added response to fluoxetine GO:0014076 has child of organic cyclic substance
Do we all agree with this?<br>
 
We agree to add synonyms for better describe the use of a substance.<br>
 
4) fill in the Dbxrefs with the ChEBI ID correspondent to the term in the ChEBI ontology.<br>
 
5) what about "response to xenobiotic stimulus" GO:0009410? do we want to obsolete it? [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1494548&group_id=36855| SF 1494548] on xenobiotic terms<br>
 
We have to be very careful about that.<br>
 

Latest revision as of 15:25, 6 March 2020

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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:

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