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Symptom Ontology Wiki

Welcome to the Symptom Ontology Community Wiki. The Symptom Ontology was developed as part of the Gemina project starting in 2005 at TIGR. Work continues on the project at the Institute for Genome Sciences (IGS) at the University of Maryland.

• The Symptom Ontology is organized primary by body regions with a branch for general symptoms.
• The Symptoms Ontology in July 2008 was submitted for inclusion and review to the OBO Foundry.
• This project is open to collaborative development. Please contact the project PI, Lynn Schriml at: lynn.schriml@gmail.com.

Scope

• The symptom ontology was designed around the guiding concept of a symptom being: "A perceived change in function, sensation or appearance reported by a patient indicative of a disease".
• Understanding the close relationship of Signs and Symptoms, where Signs are the objective observation of an illness, the Symptom Ontology will work to broaden it's scope to capture and document in a more robust manor these two sets of terms. Understanding that at times, the same term may be both a Sign and a Symptom.

Meetings

• Signs, Symptoms and Findings: http://bioontology.org/wiki/index.php/DallasWorkshop
  • At the September, 2008 meeting many presenters described how in clinical practice Signs and Symptoms are distinct entities of terms.
  • At this meeting, Larry Streepy of the Cleveland Clinic proposed that in order to integrate Signs and Symptoms into one ontology that the observer must be recorded. This point was well supported at the meeting, including Sivaram Arabandi, also of the Cleveland Clinic.
• IDO: Infectious Disease Ontology Meeting: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology_2008

Ongoing Developement

• Review of the current version of the Symptom Ontology shows that there are terms that are disorders, phenotypes and signs.
• Cross Products: One area of development for the Symptom Ontology will be to identify cross products, such as phenotype and anatomy terms and to create dbxrefs for these terms.
• SIGNS: One proposal for this area of the ontology is to create a new relation: observed_by
• Linking Symptoms and Diseases:
  • SYMPTOM: symptom_of
  • Creation of a this new relation is a possibility: symptom_of and then a db_ref for a disease to link symptoms and their known diseases.
  • SYMPTOM:hasClinicalFinding
    • Symptom = ClinicalFinding that observedBy some Patient
    • Sign = ClinicalFinding that observedBy some Physician
  • Symptom term:has_property: sign and symptom
    • this property: use this property for the case where a term is both a sign and a symptom
  • DISEASE: some ideas for properties of diseases in the Disease Ontology.
    • hasClinicalFinding [symptom] OR hasClinicalSymptom [symptom]

Collaborators

• Warren Kibbe, Northwestern
• Saul Fuentes, Colorado State University
• Sivaram Arabandi, Cleveland Clinic

Related Links

• Symptom Ontology in Sourceforge: http://gemina.svn.sourceforge.net/viewvc/gemina/trunk/Gemina/ontologies/gemina_symptom.obo?view=log
• Disease Ontology: http://diseaseontology.sourceforge.net/
• Disease Ontology Wiki: http://do-wiki.nubic.northwestern.edu/index.php/Main_Page
• OBO Foundry (Open Biomedical Ontologies): http://www.obofoundry.org/
• Gemina database: http://gemina.igs.umaryland.edu/cgi-bin/gemina/MakeFrontPages.cgi
• Institute for Genome Sciences (IGS): http://www.igs.umaryland.edu/