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Posted to user@ctakes.apache.org by "Hari, Sekhar" <se...@cgi.com> on 2017/12/07 13:04:26 UTC
RE: Drug-Allergy Contraindications [EXTERNAL]
Thank you so much. I will check that.
Just a question out of my curiosity - are Drug-Allergy (the so called ADR) the same as Drug-Gene interactions (for example: immunological reactions caused by a gene due to a particular drug substance)?
Thanks,
Sekhar H.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: 07 December 2017 18:30
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Hi Sekhar H.,
You could check out the downloads at openfda.gov
https://open.fda.gov/downloads/
The json files in food/event and drug/event might help.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 7:38 AM
To: user@ctakes.apache.org; dev@ctakes.apache.org
Subject: Drug-Allergy Contraindications [EXTERNAL]
Hi -
Is anybody aware of a database that stores all reported drug-allergy contraindications?
Thanks,
Sekhar H.
RE: Drug-Allergy Contraindications [EXTERNAL] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Ooh - OMIM has released an api:
http://omim.org/api
Sean
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Thursday, December 07, 2017 8:11 AM
To: Hari, Sekhar
Cc: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL] [SUSPICIOUS]
I think that you are talking about metabolic genetics. That isn't the same thing, though there may be information in the fda drug/event or food/event, for instance for gum and soft drinks for phenylketonuria (PKU). But There may be a better way to get that information. Gene Ontology (GO) or Human Phenome Ontology (HPO)?
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 8:04 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Thank you so much. I will check that.
Just a question out of my curiosity - are Drug-Allergy (the so called ADR) the same as Drug-Gene interactions (for example: immunological reactions caused by a gene due to a particular drug substance)?
Thanks,
Sekhar H.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: 07 December 2017 18:30
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Hi Sekhar H.,
You could check out the downloads at openfda.gov
https://urldefense.proofpoint.com/v2/url?u=https-3A__open.fda.gov_downloads_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=iaiNRnm2HC44M__BYtKd7n-ykF_rhlKbAMBXpvpx73A&s=u7jx7Tlezy5T_AsqaB6MWeBAfoVPik_F5LZ3ukwwHZU&e=
The json files in food/event and drug/event might help.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 7:38 AM
To: user@ctakes.apache.org; dev@ctakes.apache.org
Subject: Drug-Allergy Contraindications [EXTERNAL]
Hi -
Is anybody aware of a database that stores all reported drug-allergy contraindications?
Thanks,
Sekhar H.
FW: Drug-Allergy Contraindications [EXTERNAL]
Posted by "Hari, Sekhar" <se...@cgi.com>.
Hi -
I' m looking to build a drug-allergy alert system. For example, for a Type A adverse drug reactions (e.g. 'Patient is allergic to Penicillin') - so we take in parameters for the allergy (Penicillin) and the drug (Amoxicillin), and returns a warning saying not to prescribe it. Do we have anything pre-built which can be reused? Please see the email from Sean below.
Thanks
Sekhar H
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: 07 December 2017 22:50
To: Hari, Sekhar
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Hi Sekhar H.,
Ah - that is very different from a database containing reported drug allergies. Ctakes does not do that as-is. You would need to implement a component that compares the discovered medication allergies and the prescribed medications and then displays a warning. Somebody may have one pre-built that you can reuse. Otherwise it should be fairly easy to implement a rough version using section types and cui proximities, perhaps with a dash of regex for a bolder flavor. However, I would post to the dev list to see if anybody has something that would work for you.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 11:23 AM
To: Finan, Sean
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
I'm talking about type A adverse drug reactions (e.g. 'Patient is allergic to Penicillin' - so we take in parameters for the allergy (Penicillin) and the drug (Amoxicillin), and returns a warning saying not to prescribe it). Can cTAKES do this?
Thanks
Sekhar H.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: 07 December 2017 18:41
To: Hari, Sekhar
Cc: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
I think that you are talking about metabolic genetics. That isn't the same thing, though there may be information in the fda drug/event or food/event, for instance for gum and soft drinks for phenylketonuria (PKU). But There may be a better way to get that information. Gene Ontology (GO) or Human Phenome Ontology (HPO)?
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 8:04 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Thank you so much. I will check that.
Just a question out of my curiosity - are Drug-Allergy (the so called ADR) the same as Drug-Gene interactions (for example: immunological reactions caused by a gene due to a particular drug substance)?
Thanks,
Sekhar H.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: 07 December 2017 18:30
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Hi Sekhar H.,
You could check out the downloads at openfda.gov
https://urldefense.proofpoint.com/v2/url?u=https-3A__open.fda.gov_downloads_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=iaiNRnm2HC44M__BYtKd7n-ykF_rhlKbAMBXpvpx73A&s=u7jx7Tlezy5T_AsqaB6MWeBAfoVPik_F5LZ3ukwwHZU&e=
The json files in food/event and drug/event might help.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 7:38 AM
To: user@ctakes.apache.org; dev@ctakes.apache.org
Subject: Drug-Allergy Contraindications [EXTERNAL]
Hi -
Is anybody aware of a database that stores all reported drug-allergy contraindications?
Thanks,
Sekhar H.
FW: Drug-Allergy Contraindications [EXTERNAL]
Posted by "Hari, Sekhar" <se...@cgi.com>.
Hi -
I' m looking to build a drug-allergy alert system. For example, for a Type A adverse drug reactions (e.g. 'Patient is allergic to Penicillin') - so we take in parameters for the allergy (Penicillin) and the drug (Amoxicillin), and returns a warning saying not to prescribe it. Do we have anything pre-built which can be reused? Please see the email from Sean below.
Thanks
Sekhar H
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: 07 December 2017 22:50
To: Hari, Sekhar
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Hi Sekhar H.,
Ah - that is very different from a database containing reported drug allergies. Ctakes does not do that as-is. You would need to implement a component that compares the discovered medication allergies and the prescribed medications and then displays a warning. Somebody may have one pre-built that you can reuse. Otherwise it should be fairly easy to implement a rough version using section types and cui proximities, perhaps with a dash of regex for a bolder flavor. However, I would post to the dev list to see if anybody has something that would work for you.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 11:23 AM
To: Finan, Sean
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
I'm talking about type A adverse drug reactions (e.g. 'Patient is allergic to Penicillin' - so we take in parameters for the allergy (Penicillin) and the drug (Amoxicillin), and returns a warning saying not to prescribe it). Can cTAKES do this?
Thanks
Sekhar H.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: 07 December 2017 18:41
To: Hari, Sekhar
Cc: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
I think that you are talking about metabolic genetics. That isn't the same thing, though there may be information in the fda drug/event or food/event, for instance for gum and soft drinks for phenylketonuria (PKU). But There may be a better way to get that information. Gene Ontology (GO) or Human Phenome Ontology (HPO)?
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 8:04 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Thank you so much. I will check that.
Just a question out of my curiosity - are Drug-Allergy (the so called ADR) the same as Drug-Gene interactions (for example: immunological reactions caused by a gene due to a particular drug substance)?
Thanks,
Sekhar H.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: 07 December 2017 18:30
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Hi Sekhar H.,
You could check out the downloads at openfda.gov
https://urldefense.proofpoint.com/v2/url?u=https-3A__open.fda.gov_downloads_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=iaiNRnm2HC44M__BYtKd7n-ykF_rhlKbAMBXpvpx73A&s=u7jx7Tlezy5T_AsqaB6MWeBAfoVPik_F5LZ3ukwwHZU&e=
The json files in food/event and drug/event might help.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 7:38 AM
To: user@ctakes.apache.org; dev@ctakes.apache.org
Subject: Drug-Allergy Contraindications [EXTERNAL]
Hi -
Is anybody aware of a database that stores all reported drug-allergy contraindications?
Thanks,
Sekhar H.
RE: Drug-Allergy Contraindications [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
I think that you are talking about metabolic genetics. That isn't the same thing, though there may be information in the fda drug/event or food/event, for instance for gum and soft drinks for phenylketonuria (PKU). But There may be a better way to get that information. Gene Ontology (GO) or Human Phenome Ontology (HPO)?
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 8:04 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Thank you so much. I will check that.
Just a question out of my curiosity - are Drug-Allergy (the so called ADR) the same as Drug-Gene interactions (for example: immunological reactions caused by a gene due to a particular drug substance)?
Thanks,
Sekhar H.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: 07 December 2017 18:30
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Hi Sekhar H.,
You could check out the downloads at openfda.gov
https://urldefense.proofpoint.com/v2/url?u=https-3A__open.fda.gov_downloads_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=iaiNRnm2HC44M__BYtKd7n-ykF_rhlKbAMBXpvpx73A&s=u7jx7Tlezy5T_AsqaB6MWeBAfoVPik_F5LZ3ukwwHZU&e=
The json files in food/event and drug/event might help.
Sean
-----Original Message-----
From: Hari, Sekhar [mailto:sekhar.hari@cgi.com]
Sent: Thursday, December 07, 2017 7:38 AM
To: user@ctakes.apache.org; dev@ctakes.apache.org
Subject: Drug-Allergy Contraindications [EXTERNAL]
Hi -
Is anybody aware of a database that stores all reported drug-allergy contraindications?
Thanks,
Sekhar H.