Update, 13 June 2024: I am updating this repository to be compatible with the Ontology Development Kit (ODK). This means major changes to the layout of this repository to be in-line with the ODK template in order to not lose the Git history or require individuals to go to another page to find the GSSO. Please rest assured, I am working on getting everything up-to-date as soon as possible to prevent errors and confusion.

Update, 24 October 2023: I have been engaging in efforts to expand the GSSO in a format more easily accessible to those without significant programming, database, or ontology experience. I have settled on using a Wikibase setup to attain these goals. So far I have been prototyping this structure here. I am still seeking a source of funding in order to work on the database and vocabulary full-time; please feel free to reach out to me if there are any suggestions you may have regarding full-time funding or positions in which I could continue this work full-time. This new work will include a complete mapping to all versions of the GSSO, meaning all usage of the current GSSO elements will remain intact. Please do not hesitate to reach out if you have any comments, questions, or concerns.

Gender, Sex, and Sexual Orientation

The Gender, Sex, and Sexual Orientation (GSSO) ontology is an ontology which includes a vast amount of information related to gender identity, gender expression, romantic identity, sexual identity, sexual orientation, sexual behavior, sexual abuse, and various related topics. Its emphasis is on a multidisciplinary and intersectional approach to these topics.

Usage

If you would like to use the raw OWL files here, it is recommended that you download the Protégé program here and open it in that program. Alternatively you can access the system via the NCBO BioPortal API (explained below) or via our website: https://gsso.research.cchmc.org/. It is recommended to use the OWL format (which is RDF/XML from 2.0.5 onward).

If you use the GSSO in your projects, we would really appreciate the citation! Please use the most recent publication under "Publications - GSSO Publications".

As An Educational Tool

The GSSO's stand-alone website at CCHMC (https://gsso.research.cchmc.org/) is meant as the most accessible site for referencing individual terms for educational purposes. We are always accepting suggestions on how this interface can be improved, or collaborations we can contribute to!

As Subject Headings

The GSSO has entered a pilot phase for usage at subject headings with the GLBT Museum & Archives. If you are interested in similar usage, please contact the author(s) at the email below!

Generally, we recommend using the label or alternate name attributes, we the IRI in parenthetical afterward. This makes it easier to see during web scraping (if a centralized database is theoretically created) regardless of system used when entering subject heading guides.

As A Natural Language Processing (NLP) Instrument

If you are planning on using the GSSO for NLP, please contact the authors! While the scripts are currently not available on the GitHub, we can share some of our scripts (written in Python3) via email if you would like!

We recommend downplaying related synonyms and short names, for instance, as these are often ambiguous in nature.

Translating the GSSO

If you are interested in translating the GSSO, please let us know! Contact the author(s) below if you are engaging in translation.

Website

The GSSO is separately available at Ontobee here, at the NCBO BioPortal here, EMBL-EBI OLS here. However, there is also a stand-alone website hosted at Cincinnati Children's Hospital and Medical Center (CCHMC), here.

These sites update periodically based on this GitHub repository. This means that the GitHub is the only resource that is guaranteed to be up-to-date.

At the stand-alone site, there is a text annotation feature. Other similar annotation features are available at the NCBO BioPortal and Ontobee.

API Access

The API for the GSSO can be accessed as part of the NCBO BioPortal's API. For more information, consult the NCBO BioPortal API documentation here. Note that first you must create an NCBO BioPortal account and obtain an API key, in order for most of these calls to work.

The GSSO can also be accessed using Ontobee's SPARQL query interface here.

Getting Instances for a Class

In order to get instances for a given class, the BioPortal concept ID should be created from the class ID. After 2.0.4, URIs were changed to be OBO Foundry compliant. All IDs all the same, but the rest of the URI has changed, i.e.:

http://purl.bioontology.org/ontology/GSSO/000047

And

http://purl.bioontology.org/ontology/GSSO/GSSO_000047

Are now rendered as:

http://purl.obolibrary.org/obo/GSSO_000047

Because the BioPortal system requires encoded URLs, we will shift this into:

http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGSSO_000047

This can also be accomplished using any URL encoder, such as: https://www.urlencoder.org/.

This is why the normal NCBO BioPortal link is rendered as:

https://bioportal.bioontology.org/ontologies/GSSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGSSO_000047

(however, note that https://bioportal.bioontology.org/ontologies/GSSO/?p=classes&conceptid=http://purl.obolibrary.org/obo/GSSO_000047 will also work.)

The full URL for access to the class is thus:

http://data.bioontology.org/ontologies/GSSO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGSSO_000047/

Note that this method will only grab instances from the current class, not from subclasses; i.e. the following:

http://data.bioontology.org/ontologies/GSSO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGSSO_000140/instances

Will pull LGBTQ slang, but not transgender slang.

Note that if any of the following queries do not function, reattempt with just the identifier and note the full URL. Alternatively use the URL as a search term via the GSSO website itself if problems persist.

For instance, the Homosaurus link mapping can be obtained using:

https://gsso.research.cchmc.org/#!/entry?iri=http://homosaurus.org/v2/LGBTQPeople

on the website.

Getting GSSO from Homosaurus

Simply use the Homosaurus URI in the q parameter, for instance with http://homosaurus.org/v2/LGBTQPeople:

http://data.bioontology.org/search?q=http://homosaurus.org/v2/LGBTQPeople&ontologies=GSSO&also_search_properties=true

Getting GSSO from LCSH

Obtain an LCSH URI, such as http://id.loc.gov/authorities/subjects/sh2007003708 and add it as follows:

http://data.bioontology.org/search?q=http://id.loc.gov/authorities/subjects/sh2007003708&ontologies=GSSO&also_search_properties=true

Getting GSSO from LCC

Getting the entry for "RC571" is implemented as follows:

http://data.bioontology.org/search?q=RC571&ontologies=GSSO&also_search_properties=true

Getting GSSO from MeSH

MeSH such as http://purl.bioontology.org/ontology/MESH/D063106 can be obtained with:

http://data.bioontology.org/search?q=http://purl.bioontology.org/ontology/MESH/D063106&ontologies=GSSO&also_search_properties=true

Getting GSSO from Wikipedia

If you have a Wikipedia page URL or a Wikidata URL, you can attempt to add it as follows:

http://data.bioontology.org/search?q=https://en.wikipedia.org/wiki/Document&ontologies=GSSO&also_search_properties=true

Getting GSSO from NCI Thesaurus

If you have an identifier such as C19498, simply append it to http://purl.obolibrary.org/obo/NCIT_, then form the query as follows:

http://data.bioontology.org/search?q=http://purl.obolibrary.org/obo/NCIT_C19498&ontologies=GSSO&also_search_properties=true

Getting GSSO from SNOMED-CT

If you have a SNOMED-CT identifier, such as 302960008, append it to http://purl.bioontology.org/ontology/SNOMEDCT/ and run the following:

http://data.bioontology.org/search?q=http://purl.bioontology.org/ontology/SNOMEDCT/302960008&ontologies=GSSO&also_search_properties=true

Versioning

Note that versions with "rdf_xml" in the title are in RDF/XML format, while those without utilize Manchester OWL syntax.

Further, note that PURLs utilize the "1.0.1" syntax as to be backwards compatible with any of the 1.0.1 releases. The 1.0.0 release is not forward or backward compatible at the present time. It is recommended that users utilize 2.0.0.

Version 2.0.1 was created in an attempt to fix PURLs within the NCBO BioPortal version of GSSO so as to be more accessible, but it did not load as expected. We are in contact with the NCBO BioPortal team to attempt to fix this. Version 2.0.2 was another failed attempt, and does not function correctly (and therefore has not been updated).

Version 2.0.3 returns to the 2.0.0 PURLs and includes additional new Homosaurus mappings, mappings from the Leather Archives and Museum (LA&M), and mappings from the GLBT Historical Society's Archives.

Versions 2.0.4 and onward switch to OBO Foundry compliant PURLs, which will be maintained for all future versions.

Version 2.0.6 is an intermediate version, adding a number of terms from the backlog of needed additions, as well as touching up a number of existing entries. It is still a work-in-progress and do not yet contain full mappings to versions 1 and 3 of the Homosaurus.

Version 2.0.7 is an alpha version, as the conversion to OBO format is not currently working. Please be patient as we attempt to fix the issue.

Version 2.0.8 is also in alpha, with only a couple small changes based on reported issues. Conversion to JSON and OBO formats has not been possible, so those files are still version 2.0.7 as of 8 July 2022.

• 1.0.0 (24 June 2019)
• 1.0.1a (11 September 2019)
• 1.0.1b (12 September 2019)
• 1.0.1c (13 September 2019)
• 1.0.1d (13 September 2019)
• 1.0.1e (13 September 2019)
• 2.0.0 (18 June 2020)
• 2.0.1 (22 July 2020)
• 2.0.2 (N/A)
• 2.0.3 (N/A)
• 2.0.4 (N/A)
• 2.0.5 (N/A)
• 2.0.6 (15 October 2021)
• 2.0.7 (22 December 2021)
• 2.0.8 (8 July 2022)
• 2.0.9 (6 September 2022)
• 2.0.10 (8 September 2022)

Contributing

Please feel free to contribute! If there is a term or terms that include unsatisfactory information, broken links, derogatory terminology that is not appropriately marked, please contact us! Additionally, we are attempting to include as much information from disparate archives as possible. If you or someone you know runs an LGBTQIA+ and/or sex archive with a controlled terminology, let us know!

A very basic search/browse interface of version 1.0.0 was located here. This site has been deprecated as of 2020. A new demo site is available here.

An alpha version of 2.0.4 is also available on the NCBO BioPortal here.

There is also a survey going over various features of the GSSO here if you have time to rate the GSSO!

Authors

• Clair Kronk ([email protected])

License

This project and any associated software created as part of the GSSO system are currently bound by the Apache 2.0 License. The GSSO ontology itself is bound by the CC BY-NC-ND 4.0 license. All mapped ontologies within GSSO are within Creative Commons, but may require separate requirements. Please check with their respective creators before utilizing.

Publications

GSSO Publications

• Kronk C. ''Gender, Sex and Sexual Orientation in Medicine: A Linguistic Analysis'' (2021). University of Cincinnati School of Medicine. Ph.D. Thesis. Permalink: ucin1617107411106107.

• Kronk C, Dexheimer J. "Development of the Gender, Sex, and Sexual Orientation Ontology: Evaluation and Workflow." Journal of the American Medical Informatics Association. 2020. DOI: 10.1093/jamia/ocaa061. PMID: 32548638.

• Kronk C, Tran G, Wu D. "Creating a Queer Ontology: Introduction of the Gender, Sex, and Sexual Orientation (GSSO) Ontology." MEDINFO 2019: Health and Wellbeing e-Networks for All. 2019:264. DOI: 10.3233/SHTI190213. PMID: 31437915.

Publications Which Utilize/Cite the GSSO

If you've published something that uses the GSSO, please contact us! We'd love to add your work here!

• Lynch, K, Alba P, Patterson O, Viernes B, Coronado G, DuVall S. "The Utility of Clinical Notes for Sexual Minority Health Research." American Journal of Preventive Medicine. 2020. DOI: 10.1016/j.amepre.2020.05.026. PMID: 33011005

• Tai, J. "Cultural Humility as a Framework for Anti-Oppressive Archival Description." Journal of Critical Library and Information Studies. 2020.

Projects

Projects Which Utilize/Cite the GSSO

• EMERSE (Electronic Medical Record Search Engine) Synonyms
• GLBT Historical Society, Online Archive of California

Resources

Resources Which Link to the GSSO

• Dictionaries, Glossaries, Ontologies, and Guides at New York University (NYU) Libraries Gender and Sexuality Studies Research Guide

Acknowledgments

• Judith W. Dexheimer
• Mark H. Eckman
• Giao Q. Tran
• Danny T. Y. Wu