Difference between revisions of "Ontology"

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==Introduction to OWL ontology==
 
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In the summer of 2017, we began the process of converting portions of the HemOnc.org website content into a formal [https://www.w3.org/OWL/ OWL ontology], along with some additional external information such as RxNorm identifiers. As of the last release ('''2018-10-29'''), the ontology contains information on:
 
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*'''Diseases:''' names, classifications
 
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*'''Interventions''', in four major classes:
 
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**'''Biologic products:''' factor replacement, cellular therapy, etc.
 
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**'''Devices'''
 
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**'''Drugs:''' names, synonyms, classifications, RxCUI (when available), sigs
 
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**'''Radiation'''
 
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*'''Regimens:''' names, synonyms, classifications, components, references
 
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*'''References:''' title, journal, year of publication, classifications, number of authors, authors
 
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*'''Authors:''' name
 
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For a much more detailed explanation, you can download the latest release notes here: [[File:Release notes 2018-10-29.docx]].
 
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<span style="color:red">'''Note: due to a shift to an OMOP-compatible database, we do not plan to support additional versions of the ontology in OWL, for the time being. See below.'''</span>
 
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==Introduction to HemOnc vocabulary==
 
==Introduction to HemOnc vocabulary==
 
In late 2018, we began to work closely with the [https://www.ohdsi.org/ OHDSI Oncology Subgroup] to transition from the existing OWL format to the widely-used OMOP format. The first phase of this work was completed in June 2019 and a portion of the HemOnc vocabulary has been released to the public through the [http://athena.ohdsi.org/search-terms/terms ATHENA] tool.You can see how this looks by searching for "GemOx" using [http://athena.ohdsi.org/search-terms/terms?query=gemox&page=1 this link]. [https://twitter.com/hemoncwarner/status/1139250410454245377 More details here].
 
In late 2018, we began to work closely with the [https://www.ohdsi.org/ OHDSI Oncology Subgroup] to transition from the existing OWL format to the widely-used OMOP format. The first phase of this work was completed in June 2019 and a portion of the HemOnc vocabulary has been released to the public through the [http://athena.ohdsi.org/search-terms/terms ATHENA] tool.You can see how this looks by searching for "GemOx" using [http://athena.ohdsi.org/search-terms/terms?query=gemox&page=1 this link]. [https://twitter.com/hemoncwarner/status/1139250410454245377 More details here].
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# Warner JL, Dymshyts D, Reich CG, Gurley MJ, Hochheiser H, Moldwin ZH, Belenkaya R, Williams AE, Yang PC. HemOnc: a new standard vocabulary for chemotherapy regimen representation in the OMOP Common Data Model. J Biomed Inform. 2019 Aug;96:103239. Epub 2019 Jun 22. [https://www.sciencedirect.com/science/article/pii/S1532046419301583 link to SD article] [https://www.ncbi.nlm.nih.gov/pubmed/31238109 PubMed]
 
# Warner JL, Dymshyts D, Reich CG, Gurley MJ, Hochheiser H, Moldwin ZH, Belenkaya R, Williams AE, Yang PC. HemOnc: a new standard vocabulary for chemotherapy regimen representation in the OMOP Common Data Model. J Biomed Inform. 2019 Aug;96:103239. Epub 2019 Jun 22. [https://www.sciencedirect.com/science/article/pii/S1532046419301583 link to SD article] [https://www.ncbi.nlm.nih.gov/pubmed/31238109 PubMed]
 
# This work is currently supported in part by National Institutes of Health (NIH) Grants No. [http://grantome.com/grant/NIH/U24-CA194215-01A1 U24 CA194215], and [http://grantome.com/grant/NIH/U01-CA231840-01 U01 CA231840]. Previously, this work was supported by NIH Grant No. L30 CA171123 and [http://grantome.com/grant/NIH/U24-CA184407-01 U24 CA184407]. Portions of this work were conducted using the [https://protege.stanford.edu/ Protégé resource], which is supported by Grant No. GM10331601 from the NIH National Institute of General Medical Sciences.
 
# This work is currently supported in part by National Institutes of Health (NIH) Grants No. [http://grantome.com/grant/NIH/U24-CA194215-01A1 U24 CA194215], and [http://grantome.com/grant/NIH/U01-CA231840-01 U01 CA231840]. Previously, this work was supported by NIH Grant No. L30 CA171123 and [http://grantome.com/grant/NIH/U24-CA184407-01 U24 CA184407]. Portions of this work were conducted using the [https://protege.stanford.edu/ Protégé resource], which is supported by Grant No. GM10331601 from the NIH National Institute of General Medical Sciences.
 +
 +
==Introduction to OWL ontology (historical)==
 +
In the summer of 2017, we began the process of converting portions of the HemOnc.org website content into a formal [https://www.w3.org/OWL/ OWL ontology], along with some additional external information such as RxNorm identifiers. As of the last release ('''2018-10-29'''), the ontology contains information on:
 +
 +
*'''Diseases:''' names, classifications
 +
*'''Interventions''', in four major classes:
 +
**'''Biologic products:''' factor replacement, cellular therapy, etc.
 +
**'''Devices'''
 +
**'''Drugs:''' names, synonyms, classifications, RxCUI (when available), sigs
 +
**'''Radiation'''
 +
*'''Regimens:''' names, synonyms, classifications, components, references
 +
*'''References:''' title, journal, year of publication, classifications, number of authors, authors
 +
*'''Authors:''' name
 +
 +
For a much more detailed explanation, you can download the latest release notes here: [[File:Release notes 2018-10-29.docx]].
 +
 +
<span style="color:red">'''Note: due to a shift to an OMOP-compatible database, we do not plan to support additional versions of the ontology in OWL, for the time being. See below.'''</span>
  
 
[[Category:General reference pages]]
 
[[Category:General reference pages]]

Revision as of 21:53, 21 January 2020

Introduction to HemOnc vocabulary

In late 2018, we began to work closely with the OHDSI Oncology Subgroup to transition from the existing OWL format to the widely-used OMOP format. The first phase of this work was completed in June 2019 and a portion of the HemOnc vocabulary has been released to the public through the ATHENA tool.You can see how this looks by searching for "GemOx" using this link. More details here.

The OMOP model is built on concept and relationship tables. Please use the links to learn more about what concepts and relationships are currently included in the vocabulary.

Availability

Beyond what is available through ATHENA, the full ontology is freely available for academic or non-commercial use, upon request. We are also willing to discuss commercial uses on a case-by-case basis. Please let us know of your interest by sending an email ([email protected]).

Academic and Non-Commcercial License

The full HemOnc.org ontology is licensed by version under the CreativeCommons NonCommercial-ShareAlike 4.0 International License for academic and non-commercial users. Under this license, users are free to:

  • Share — copy and redistribute the material in any medium or format
  • Adapt — remix, transform, and build upon the material

Under the following terms:

  • Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
  • NonCommercial — You may not use the material for commercial purposes.
  • ShareAlike — If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.
  • No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.

References and acknowledgements

  1. Malty AM, Jain SK, Yang PC, Harvey K, Warner JL. Computerized approach to creating a systematic ontology of hematology/oncology regimens. JCO Clin Cancer Inform. 2018 May 11. link to original article link to PMC article PubMed
  2. Warner JL, Dymshyts D, Reich CG, Gurley MJ, Hochheiser H, Moldwin ZH, Belenkaya R, Williams AE, Yang PC. HemOnc: a new standard vocabulary for chemotherapy regimen representation in the OMOP Common Data Model. J Biomed Inform. 2019 Aug;96:103239. Epub 2019 Jun 22. link to SD article PubMed
  3. This work is currently supported in part by National Institutes of Health (NIH) Grants No. U24 CA194215, and U01 CA231840. Previously, this work was supported by NIH Grant No. L30 CA171123 and U24 CA184407. Portions of this work were conducted using the Protégé resource, which is supported by Grant No. GM10331601 from the NIH National Institute of General Medical Sciences.

Introduction to OWL ontology (historical)

In the summer of 2017, we began the process of converting portions of the HemOnc.org website content into a formal OWL ontology, along with some additional external information such as RxNorm identifiers. As of the last release (2018-10-29), the ontology contains information on:

  • Diseases: names, classifications
  • Interventions, in four major classes:
    • Biologic products: factor replacement, cellular therapy, etc.
    • Devices
    • Drugs: names, synonyms, classifications, RxCUI (when available), sigs
    • Radiation
  • Regimens: names, synonyms, classifications, components, references
  • References: title, journal, year of publication, classifications, number of authors, authors
  • Authors: name

For a much more detailed explanation, you can download the latest release notes here: File:Release notes 2018-10-29.docx.

Note: due to a shift to an OMOP-compatible database, we do not plan to support additional versions of the ontology in OWL, for the time being. See below.

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