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Monarch web application and API
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Clinical pathology reports as phenotype #584

Open selewis opened 9 years ago

selewis commented 9 years ago

I think it would be very helpful to extend HPO to include more terms/synonyms that are commonly used in clinical pathology reports. For example, diabetes mellitus includes hyperglycemia (HP) as one of its phenotypes, which is great, but "high serum glucose measurement", "glucose challenge low" (or high), are not included as related/relevant synonyms. For mining EHRs (obtaining data from EHRs), and for people searching for things it would be useful to add more of these.

More confusion. Can find both "increased circulating glucose level" (MP) and "high blood glucose levels" (MP) and "Increased Blood Glucose Level" (HP synonym of hyperglycemia). No graph view makes it easy to chase around in circles (while leaving breadcrumbs on a piece of note paper nearby)

drseb commented 9 years ago

Hi,

I think it would be very helpful to extend HPO to include more terms/synonyms that are commonly used in clinical pathology reports. For example, diabetes mellitus includes hyperglycemia (HP) as one of its phenotypes, which is great, but "high serum glucose measurement", "glucose challenge low" (or high), are not included as related/relevant synonyms. For mining EHRs (obtaining data from EHRs), and for people searching for things it would be useful to add more of these.

I am happy to add more classes to HPO if you send me a list. You can also use the sourceforge tracker. Last but not least there is a phenotype-editors-list (phenotype-ontologies-editors@googlegroups.com), where MP and HP are coordinating their efforts.

More confusion. Can find both "increased circulating glucose level" (MP) and "high blood glucose levels" (MP) and "Increased Blood Glucose Level" (HP synonym of hyperglycemia). No graph view makes it easy to chase around in circles (while leaving breadcrumbs on a piece of note paper nearby)

MP seems to make a distinction between here between an increased form and a pathologically increased form. But this is definitely something for the phenotype-editors-list. I think you are right in that there is no dedicated graphview tool for this.

Best, Sebastian=

selewis commented 9 years ago

I'll look for a list of standard clinical report terms. I tried yesterday, but wasn't successful after ~15 minutes, apparently it might be a hospital to hospital "standard".

-S

On Wed, Nov 5, 2014 at 12:38 AM, Sebastian notifications@github.com wrote:

Hi,

I think it would be very helpful to extend HPO to include more terms/synonyms that are commonly used in clinical pathology reports. For example, diabetes mellitus includes hyperglycemia (HP) as one of its phenotypes, which is great, but "high serum glucose measurement", "glucose challenge low" (or high), are not included as related/relevant synonyms. For mining EHRs (obtaining data from EHRs), and for people searching for things it would be useful to add more of these.

I am happy to add more classes to HPO if you send me a list. You can also use the sourceforge tracker. Last but not least there is a phenotype-editors-list (phenotype-ontologies-editors@googlegroups.com), where MP and HP are coordinating their efforts.

More confusion. Can find both "increased circulating glucose level" (MP) and "high blood glucose levels" (MP) and "Increased Blood Glucose Level" (HP synonym of hyperglycemia). No graph view makes it easy to chase around in circles (while leaving breadcrumbs on a piece of note paper nearby)

MP seems to make a distinction between here between an increased form and a pathologically increased form. But this is definitely something for the phenotype-editors-list. I think you are right in that there is no dedicated graphview tool for this.

Best, Sebastian=

— Reply to this email directly or view it on GitHub https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61775197 .

pnrobinson commented 9 years ago

This is not a particular problem, and if there are standard phrases, they can be entered as SYNONYM or whatever is appropriate. What though is the use case? Are the pathology reports going to be text mined? -Peter

nlwashington commented 9 years ago

I’ve been told by a certain someone that there’s lots of terms that can be mined out of http://mtsamples.com/ to flesh out synonyms and create new terms. Is there a student or postdoc that could work on that?

On Nov 5, 2014, at 11:29 AM, Peter Robinson notifications@github.com wrote:

This is not a particular problem, and if there are standard phrases, they can be entered as SYNONYM or whatever is appropriate. What though is the use case? Are the pathology reports going to be text mined? -Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: selewis [notifications@github.com] Gesendet: Mittwoch, 5. November 2014 16:50 An: monarch-initiative/monarch-app Betreff: Re: [monarch-app] Clinical pathology reports as phenotype (#584)

I'll look for a list of standard clinical report terms. I tried yesterday, but wasn't successful after ~15 minutes, apparently it might be a hospital to hospital "standard".

-S

On Wed, Nov 5, 2014 at 12:38 AM, Sebastian notifications@github.com wrote:

Hi,

I think it would be very helpful to extend HPO to include more terms/synonyms that are commonly used in clinical pathology reports. For example, diabetes mellitus includes hyperglycemia (HP) as one of its phenotypes, which is great, but "high serum glucose measurement", "glucose challenge low" (or high), are not included as related/relevant synonyms. For mining EHRs (obtaining data from EHRs), and for people searching for things it would be useful to add more of these.

I am happy to add more classes to HPO if you send me a list. You can also use the sourceforge tracker. Last but not least there is a phenotype-editors-list (phenotype-ontologies-editors@googlegroups.com), where MP and HP are coordinating their efforts.

More confusion. Can find both "increased circulating glucose level" (MP) and "high blood glucose levels" (MP) and "Increased Blood Glucose Level" (HP synonym of hyperglycemia). No graph view makes it easy to chase around in circles (while leaving breadcrumbs on a piece of note paper nearby)

MP seems to make a distinction between here between an increased form and a pathologically increased form. But this is definitely something for the phenotype-editors-list. I think you are right in that there is no dedicated graphview tool for this.

Best, Sebastian=

— Reply to this email directly or view it on GitHub https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61775197 .

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61828333. — Reply to this email directly or view it on GitHub.

selewis commented 9 years ago

Yes, apparently some groups are mining EHR with these, thinking that focusing solely on the pathology reports might be most useful in interpretation GWAS-y&PheWas-y.

On Wed, Nov 5, 2014 at 8:29 AM, Peter Robinson notifications@github.com wrote:

This is not a particular problem, and if there are standard phrases, they can be entered as SYNONYM or whatever is appropriate. What though is the use case? Are the pathology reports going to be text mined? -Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: selewis [notifications@github.com] Gesendet: Mittwoch, 5. November 2014 16:50 An: monarch-initiative/monarch-app Betreff: Re: [monarch-app] Clinical pathology reports as phenotype (#584)

I'll look for a list of standard clinical report terms. I tried yesterday, but wasn't successful after ~15 minutes, apparently it might be a hospital to hospital "standard".

-S

On Wed, Nov 5, 2014 at 12:38 AM, Sebastian notifications@github.com wrote:

Hi,

I think it would be very helpful to extend HPO to include more terms/synonyms that are commonly used in clinical pathology reports. For example, diabetes mellitus includes hyperglycemia (HP) as one of its phenotypes, which is great, but "high serum glucose measurement", "glucose challenge low" (or high), are not included as related/relevant synonyms. For mining EHRs (obtaining data from EHRs), and for people searching for things it would be useful to add more of these.

I am happy to add more classes to HPO if you send me a list. You can also use the sourceforge tracker. Last but not least there is a phenotype-editors-list (phenotype-ontologies-editors@googlegroups.com), where MP and HP are coordinating their efforts.

More confusion. Can find both "increased circulating glucose level" (MP) and "high blood glucose levels" (MP) and "Increased Blood Glucose Level" (HP synonym of hyperglycemia). No graph view makes it easy to chase around in circles (while leaving breadcrumbs on a piece of note paper nearby)

MP seems to make a distinction between here between an increased form and a pathologically increased form. But this is definitely something for the phenotype-editors-list. I think you are right in that there is no dedicated graphview tool for this.

Best, Sebastian=

— Reply to this email directly or view it on GitHub < https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61775197>

.

— Reply to this email directly or view it on GitHub< https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61828333>.

— Reply to this email directly or view it on GitHub https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61835678 .

pnrobinson commented 9 years ago

Can we get a list of these synonyms -Peter

selewis commented 9 years ago

Unfortunately it was just through reading a paper (i.e. they didn't offer much and it would be manual). What I was wondering is whether there are some/any sort of existing standards for pathologists we might pull from and then do the usual text-mining+manual extensions. Maybe not worth the effort, it simply occurred to me when I was reading the paper and then used the text from one of the examples in a figure to search monarch and got zero hits (It was something about glucose levels).

-S

On Wed, Nov 5, 2014 at 10:33 PM, Peter Robinson notifications@github.com wrote:

Can we get a list of these synonyms-Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: selewis [notifications@github.com] Gesendet: Mittwoch, 5. November 2014 20:46 An: monarch-initiative/monarch-app Cc: Robinson, Peter Betreff: Re: [monarch-app] Clinical pathology reports as phenotype (#584)

Yes, apparently some groups are mining EHR with these, thinking that focusing solely on the pathology reports might be most useful in interpretation GWAS-y&PheWas-y.

On Wed, Nov 5, 2014 at 8:29 AM, Peter Robinson notifications@github.com wrote:

This is not a particular problem, and if there are standard phrases, they can be entered as SYNONYM or whatever is appropriate. What though is the use case? Are the pathology reports going to be text mined? -Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: selewis [notifications@github.com] Gesendet: Mittwoch, 5. November 2014 16:50 An: monarch-initiative/monarch-app Betreff: Re: [monarch-app] Clinical pathology reports as phenotype (#584)

I'll look for a list of standard clinical report terms. I tried yesterday, but wasn't successful after ~15 minutes, apparently it might be a hospital to hospital "standard".

-S

On Wed, Nov 5, 2014 at 12:38 AM, Sebastian notifications@github.com wrote:

Hi,

I think it would be very helpful to extend HPO to include more terms/synonyms that are commonly used in clinical pathology reports. For example, diabetes mellitus includes hyperglycemia (HP) as one of its phenotypes, which is great, but "high serum glucose measurement", "glucose challenge low" (or high), are not included as related/relevant synonyms. For mining EHRs (obtaining data from EHRs), and for people searching for things it would be useful to add more of these.

I am happy to add more classes to HPO if you send me a list. You can also use the sourceforge tracker. Last but not least there is a phenotype-editors-list (phenotype-ontologies-editors@googlegroups.com),

where MP and HP are coordinating their efforts.

More confusion. Can find both "increased circulating glucose level" (MP) and "high blood glucose levels" (MP) and "Increased Blood Glucose Level" (HP synonym of hyperglycemia). No graph view makes it easy to chase around in circles (while leaving breadcrumbs on a piece of note paper nearby)

MP seems to make a distinction between here between an increased form and a pathologically increased form. But this is definitely something for the phenotype-editors-list. I think you are right in that there is no dedicated graphview tool for this.

Best, Sebastian=

— Reply to this email directly or view it on GitHub <

https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61775197>

.

— Reply to this email directly or view it on GitHub<

https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61828333>.

— Reply to this email directly or view it on GitHub < https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61835678>

.

— Reply to this email directly or view it on GitHub< https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61869304>.

— Reply to this email directly or view it on GitHub https://github.com/monarch-initiative/monarch-app/issues/584#issuecomment-61933194 .