Question: Disease/Symptom Database
7
gravatar for Dirk
8.3 years ago by
Dirk80
Dirk80 wrote:

Hello!

Does anyone know of any databases that have a full list of human diseases, ailments, and their symptoms? I've tried working with UMLS, but the process of actually getting data is impossible. The Disease Ontology website is also nice, but it doesn't really have any symptoms associated with any of the diseases they have listed.

Ideas?

Edit:

cross posted on healthcare-it: http://healthcareit.stackexchange.com/questions/462

database disease • 27k views
ADD COMMENTlink modified 3.1 years ago by Emre90 • written 8.3 years ago by Dirk80

Hi, did you get a consolidated dataset with diseases and its symptoms?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by taruntater30
2
gravatar for Larry_Parnell
8.3 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Please see responses to a question I posed a couple weeks back - Know of a database of disease symptoms, preferably linking to MeSH terms?. I was provided, to date, with two good answers, from which I cannot decide on a best response, pending testing by colleagues. Nonetheless, those answers may be complementary to what is posted here.

ADD COMMENTlink modified 6 months ago by RamRS26k • written 8.3 years ago by Larry_Parnell16k

link unreachable. Do you mind updating it? (I'm interested by the answer also)

ADD REPLYlink written 14 months ago by gilga0
1
gravatar for Pierre Lindenbaum
8.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

There is a Human Phenotype Ontology: http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0000122 or even Omim.

I wonder if you could find another source of information at http://healthcareit.stackexchange.com/

ADD COMMENTlink modified 6 months ago by RamRS26k • written 8.3 years ago by Pierre Lindenbaum127k

OMIM is good, but restricted to genetic issues. Thanks for the link to the ontology wesbite--I'll have to take a look at that. Hopefully it isn't just simple descriptions of phenotype issues in humans

ADD REPLYlink written 8.3 years ago by Dirk80
1
gravatar for Alex Paciorkowski
8.3 years ago by
Rochester, NY USA
Alex Paciorkowski3.4k wrote:

Hi Dirk, This is a great question, but one where the answer is still a work in progress. Many of the large databases of information related to human disease are simply not complete, or the information is inadequately curated (or even incorrect), or not easily accessible to automated search techniques. The Human Phenotype Ontology (which Pierre mentions above) is very, very good -- however many of the terms are not formally defined, making mapping to other ontologies difficult. OMIM, while limited to genetic disease, is still vast -- but not as well-curated as it could be, and I have seen some curious conclusions drawn from mining OMIM data. These data are best reviewed with a clinician collaborator familiar with the diseases you are interested in.

Some other sources worth checking out are GeneReviews: here (although limited to single-gene conditions, but the information has a high degree of accuracy.)

Also, for neurologic conditions an interesting tool is SimulConsult, which is under constant update and is expanding to include non-neurologic and non-genetic diseases: here Its use is free, but I think you do have to register.

These are obviously small corners of human disease, but I am not aware of anything more comprehensive than UMLS and MeSH for "all of human diseases." I suspect a collaborative effort between ontologists and physician-researchers in multiple specialties will gradually organize this knowledge into the kind of dataset you are looking for.

ADD COMMENTlink written 8.3 years ago by Alex Paciorkowski3.4k
0
gravatar for Qdjm
8.3 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

I haven't looked into this in a few years but I think that it will be difficult to find a comprehensive, publicly-accessible database linking codified disease terms to codified symptoms. However, there have been some large-scale projects to collect this type of data, none of which make their data accessible, AFAIK, but maybe you can start there:

  1. Quick Medical Reference is no longer commercially available but you could try contacting the University of Pittsburgh to see whether they are willing to share the data.
  2. The Promedas project is also based on a database linking diseases to symptoms and, at one point, it was publicly funded but now it seems to have gone commercial.
  3. Another place to look is UpToDate. It's not clear that they've codified anything but they should have well-organized documents that connect diseases and symptoms.

Good luck! Please let me know if you find anything.

ADD COMMENTlink written 8.3 years ago by Qdjm1.9k
0
gravatar for Camwebb
8.0 years ago by
Camwebb10
Indonesia
Camwebb10 wrote:

Thanks for this question. One I have been pondering for a while. Please visit this post for one possible way to go ahead with an open, distributed database of diseases X symptoms.

ADD COMMENTlink written 8.0 years ago by Camwebb10
0
gravatar for Emre
3.1 years ago by
Emre90
United States
Emre90 wrote:

Hi,

Have a look at the Human symptoms–disease network. All the disease-symptoms relationships identified from text mining on Pubmed meta data and mapped to MeSH are in the supplementary data set 3.

Note that these are inferred relationships, yet reported to be fairly accurate through validation on randomly sampled and expert curated data (after some filtering). You might consider doing a filtering based on the TF-IDF scores provided in the file (>3.5 would give reasonable confidence --pretty close to P<0.05 cutoff the authors used in their analysis--).

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Emre90
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