Closed nicolevasilevsky closed 6 years ago
nicolevasilevsky
commented
6 years ago From @jmcmurry on November 17, 2017 23:5
Diagnosis requires lumbar puncture to assess CSF, which of course is extremely invasive. Note that assessing Anti-NMDA titers is easy to do but not widely available in clia-certified labs. At a minimum, immunological abnormalities could be assessed, steroids or even more aggressive immunosuppression could be appropriate until more definitive results are available.
nicolevasilevsky
commented
6 years ago From @pnrobinson on November 24, 2017 14:53
?I agree, Can we develop a file format for the common disease annotations that will include temporality and stages and environment? I will implement the format in our curation tool and then we can start to prototype this. I think there are ways of a simple extension of current formats that will allow us to develop very powerful algorithms.
-Peter
Peter Robinson?
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
10 Discovery Drive
Farmington, CT 06032
860.837.2095 t | 860.990.3130 m
peter.robinson@jax.orgmailto:peter.robinson@jax.org
www.jax.org
Robinson lab: https://robinsongroup.github.io/
New Book: Computational Exome and Genome Analysishttps://www.crcpress.com/Computational-Exome-and-Genome-Analysis/Robinson-Piro-Jager/p/book/9781498775984
The Jackson Laboratory: Leading the search for tomorrow's cures
From: Julie McMurry notifications@github.com Sent: Thursday, November 16, 2017 5:01 PM To: monarch-initiative/monarch-disease-ontology Cc: Peter Robinson; Mention Subject: [monarch-initiative/monarch-disease-ontology] Anti-NMDA Receptor Encephalitis (#419)
In terms of phenotype annotations, this disease is an excellent candidate for modeling disease staging and temporality.
It is thought that this condition is massively underdiagnosed because these folks get referred to psychiatrists instead of to neurologists. Prompt diagnosis and treatment (with immunosupressive drugs and surgical removal of teratoma if applicable) and is life-changing and life-saving.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983958/ [image]https://user-images.githubusercontent.com/3658863/32916406-d54a99ee-cad0-11e7-8a38-01ceeeb94b89.png
Mappings should include:
No suitable term in HPO yet:
Also a note for the Medical Action Ontology; terms and mappings needed for.
@pnrobinsonhttps://github.com/pnrobinson not sure what you think of those terms?
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
nicolevasilevsky
commented
6 years ago From @jmcmurry on November 24, 2017 21:50
Sounds good, Peter. Maybe I'm stating the obvious, but I'll put this out there anyway: In terms of the format for common disease staging, we probably need to be careful about distinguishing temporality (weeks/months) and staging (early, mid, late disease). Both characterizations are useful but shouldn't be conflated. In this particular case for Anti-NMDA Receptor Encephalitis, the disease progression seems to proceed along similar timeframes as far as we know now. But if you instead look at a disease like HCV the stages as defined by viral load and other signs and symptoms are much more consistent than are the actual time frames. Fulminant TB can take weeks or decades to manifest, if it does at all.
nicolevasilevsky
commented
6 years ago @jmcmurry I read the book "Brain on Fire", per your recommendation - it was really good, I enjoyed it.
@jmcmurry and @pnrobinson let me know if I can help with the common disease annotations.
nicolevasilevsky
commented
6 years ago From @pnrobinson on December 4, 2017 15:9
?Hi Nicole & everybody!
I would suggest that we start in earnest in 2018 -- let's settle on a format and a SOP and see if we can curate some diseases and do something new algorithmically with it. I would also say we should probably concentrate on one area of medicine for a start.
-peter
Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
10 Discovery Drive
Farmington, CT 06032
860.837.2095 t | 860.990.3130 m
peter.robinson@jax.orgmailto:peter.robinson@jax.org
www.jax.org
Robinson lab: https://robinsongroup.github.io/
New Book: Computational Exome and Genome Analysishttps://www.crcpress.com/Computational-Exome-and-Genome-Analysis/Robinson-Piro-Jager/p/book/9781498775984
The Jackson Laboratory: Leading the search for tomorrow's cures
From: Nicole Vasilevsky notifications@github.com Sent: Monday, December 4, 2017 7:59 AM To: monarch-initiative/monarch-disease-ontology Cc: Peter Robinson; Mention Subject: Re: [monarch-initiative/monarch-disease-ontology] Anti-NMDA Receptor Encephalitis (#419)
@jmcmurryhttps://github.com/jmcmurry I read the book "Brain on Firehttps://www.amazon.com/Brain-Fire-My-Month-Madness/dp/1451621388", per your recommendation - it was really good, I enjoyed it.
@jmcmurryhttps://github.com/jmcmurry and @pnrobinsonhttps://github.com/pnrobinson let me know if I can help with the common disease annotations.
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
nicolevasilevsky
commented
6 years ago From @cmungall on December 4, 2017 16:35
Surgical removal of tumor
We should also add a phenotype annotation to association with tumors (typically ovarian teratoma) in females? As per the ncit text def
nicolevasilevsky
commented
6 years ago From @cmungall on December 4, 2017 16:49
Do we not have an SOP for adding to the common annotations using the simpler format? E.g. making a new file in https://github.com/monarch-initiative/hpo-annotation-data/tree/master/common-diseases? Why not lets start with that.
I'm also up for using this as a test case for causal models any time. Assume we'd want to include a model of the glutamate NMDA receptor pathway
nicolevasilevsky
commented
6 years ago From @pnrobinson on December 4, 2017 16:53
Hi Chris, are you going to be in Portland next week? I think we can finalize a new format as soon as we have the chance to talk and then we can start. The previous common disease files are great as seeds but they will all need revision.
nicolevasilevsky
commented
6 years ago From @cmungall on December 4, 2017 16:54
no sorry won't be there
cmungall
commented
6 years ago @nicolevasilevsky can you summarize what the action item is and assign the relevant person. Or close the ticket
nicolevasilevsky
commented
6 years ago Sure!
Action items: 1) Julie had some new term requests for HPO, I created a ticket: https://github.com/obophenotype/human-phenotype-ontology/issues/3569. @pnrobinson - can you review this ticket, and if these terms look okay, I can add them to HPO.
2) Julie would like to annotate this disease using the new common disease annotation model. As far as I understand, that is not ready yet, right @pnrobinson? But it will be soon, is that correct?
When the new annotation tool is ready, I can create these annotations.
pnrobinson
commented
6 years ago This would be a challenging but very useful test case for the new model. Let's touch bases next week to discuss how to start. I think that the new format is ready for a v1 -- if we are willing to work on this one disease using say a google spreadsheet it would be useful to test the ideas for the format. I will start to work on code to implement the format in PhenoteFX;
nicolevasilevsky
commented
6 years ago created a new ticket in the HPO annotations repo, closing this here.
From @jmcmurry on November 16, 2017 22:1
In terms of phenotype annotations, this disease is an excellent candidate for modeling disease staging and temporality.
It is thought that this condition is massively underdiagnosed because these folks get referred to psychiatrists instead of to neurologists. Prompt diagnosis and treatment (with immunosupressive drugs and surgical removal of teratoma if applicable) and is life-changing and life-saving.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983958/
Mappings should include:
No suitable term in HPO yet:
Also a note for the Medical Action Ontology; terms and mappings needed for.
@pnrobinson not sure what you think of those terms?
Copied from original issue: monarch-initiative/monarch-disease-ontology-RETIRED#419