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updated README for MIRO guidelines formatting
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| # Ocular Immune-Mediated Inflammatory Diseases Ontology (**OcIMIDo**) | ||
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| #### See :grey_exclamation: [Issues](https://github.com/sap218/ocular-immune-mediated-inflammatory-disease-ontology/issues) for the term-tracker | ||
| #### See :grey_exclamation: [Issues](https://github.com/sap218/ocular-immune-mediated-inflammatory-disease-ontology/issues) for the term-tracker to submit a request (new term/change/suggestion) | ||
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| --- | ||
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| **Creators** | ||
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| * Samantha C Pendleton (University of Birmingham, UK ) | [samanfapc@gmail.com](mailto:samanfapc@gmail.com) | [Twitter](https://twitter.com/sap218) | [GitHub](https://github.com/sap218) | ||
| * Tasanee Braithwaite (NHS Foundation Trust, UK) | [tasaneebraithwaite@gmail.com](mailto:tasaneebraithwaite@gmail.com) | [Twitter](https://twitter.com/tasbraithwaite) | [GitHub](https://github.com/tasbraithwaite) | ||
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| --- | ||
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| **License** | ||
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| [https://creativecommons.org/licenses/by/3.0/](https://creativecommons.org/licenses/by/3.0/) - please see [LICENSE](https://github.com/sap218/ocimido/blob/master/LICENSE) for further information | ||
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| --- | ||
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| * Ontology is located in :file_folder: [`ontology`](https://github.com/sap218/ocimido/tree/master/ontology) directory | ||
| * Ontology named appropriately :page_facing_up: [`ocimido.owl`](https://github.com/sap218/ocimido/blob/master/ontology/ocimido.owl) | ||
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| **Development** | ||
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| * Ontology was built with `Protégé` | ||
| * Ontology has appropriate concepts: codes (`#OCIMIDO_00001`), class labels, comments/definitions, relationships/axioms | ||
| * Foundation based on [Royal College Clinical Dataset 2018](https://www.rcophth.ac.uk/wp-content/uploads/2014/12/Uveitis-Data-Set-Oct-2018.pdf) [RCOphth] | ||
| * Classes curated from other biomedical ontologies and included with cross-references (e.g `HPO`, `SNOMED-CT`, & more) | ||
| * Expert opinion on other missing classes | ||
| * Synonyms (layman's terms) extracted from [Olivia's Vision](http://www.oliviasvision.org/) [OV] public (open-access) forum, with permission using a tf-idf statistical analysis | ||
| Following the MIRO guidelines for reporting on an ontology [1] | ||
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| --- | ||
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| **Motivation** | ||
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| * ontology is needed because there is a lack of controlled vocabulary for eye inflammation disorders and diseases | ||
| * `DOID` and `HPO` exist however are limited: they are domain ontologies, we need an application ontology | ||
| * target audience is aimed for those who wish to use an ontology for patient-specific text (layman's terms) | ||
| **A. The basics** | ||
| * A.1 Ocular Immune-Mediated Inflammatory Diseases Ontology (OcIMIDo) v1.2.0. | ||
| * A.2 Ontology owner: Samantha C Pendleton (Institute of Cancer and Genomic Sciences, University of Birmingham, UK) [samanfapc@gmail.com](mailto:samanfapc@gmail.com). Tasanee Braithwaite (The Medical Eye Unit, St Thomas’ Hospital NHS Foundation Trust, London, UK) [tasaneebraithwaite@gmail.com](mailto:tasaneebraithwaite@gmail.com). | ||
| * A.3 [Licence](https://github.com/sap218/ocimido/blob/master/LICENSE), which governs the permissions surrounding the ontology, https://creativecommons.org/licenses/by/3.0/. | ||
| * A.4 Located in `ontology` directory: https://github.com/sap218/ocimido/blob/master/ontology/ocimido.owl. | ||
| * A.5 GitHub repository: https://github.com/sap218/ocimido. | ||
| * A.6 Methodological framework: used [Protégé](https://protege.stanford.edu/) software for ontology building and used the tf-idf statistical analysis to gain patient-preferred synonyms. | ||
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| **B. Motivation** | ||
| * B.1 Ontology is required as there currently lacks controlled vocabulary for ocular immune-mediated inflammatory diseases & the need for understanding the “patient-voice” [2]. | ||
| * B.2 OcIMIDo is derived from other biomedical ontologies, which are currently limited in the ocular domain, such as DOID, HPO, and ORDO. | ||
| * B.3 Target audience are those in the ophthalmology research area, or even extended. In additional to those who wish to create an ontology in the method we have: the quick tf-idf method. | ||
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| **C. Scope, requirements, development community** | ||
| * C.1 The requirements of the ontology is to be an extensive vocabulary for ocular-related disorders and their associated diseases. The ontology includes therapeutic interventions, investigations, symptoms, complications, genotypic data, and more. | ||
| * C.2 Development community: Samantha C Pendleton (Institute of Cancer and Genomic Sciences, University of Birmingham, UK) [samanfapc@gmail.com](mailto:samanfapc@gmail.com). Tasanee Braithwaite (The Medical Eye Unit, St Thomas’ Hospital NHS Foundation Trust, London, UK) [tasaneebraithwaite@gmail.com](mailto:tasaneebraithwaite@gmail.com). In addition to Luke T Slater (PhD), Alastair K Denniston (PhD), and Georgios V Gkoutos (PhD). | ||
| * C.3 Issue tracking system used for future developements/requests/bugs: https://github.com/sap218/ocimido/issues | ||
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| **D Knowledge acquisition** | ||
| * D.1 Foundation built from medical document, Royal College of Ophthalmology Consensus document for Uveitis [3], and experts derived list of terms to be included – and then an extensive review of current biomedical ontologies | ||
| * D.2 Medical document source https://www.rcophth.ac.uk/wp-content/uploads/2014/12/Uveitis-Data-Set-Oct-2018.pdf [3], biomedical ontologies were accessed via the ontology lookup service: https://www.ebi.ac.uk/ols/index [4]. | ||
| * D.3 Experts decided on the contents of OcIMIDo from the biomedical ontologies by searching through and extracting most relevant terms, for example, from UBERON we extracted eye-related anatomy concepts, e.g. `uvea` [UBERON:0001768]. However we avoided `iris nevus` [HP:0011525] from HPO. | ||
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| **E Ontology content** | ||
| * E.1 Ontology is `OWL/XML xmlns= "http://www.w3.org/2002/07/owl#”` - ask creator if you wish for an alternative ontology format. | ||
| * E.2 Specifically used [Protégé](https://protege.stanford.edu/) to develop the ontology with Git version control. | ||
| * E.3 Ontology metrics, as of 14-06-2020 version 1.2.0 (see [`CHANGELOG.md`](https://github.com/sap218/ocimido/blob/master/CHANGELOG.md)) there are a total of 661 classes, 1661 relationships and axioms, 2851 annotations, including 1131 database cross-references, and 187 patient-preferred synonyms. | ||
| * E.4 Cross-references ontologies inclue: DOID [5], HPO [6], ORDO [7], PATO [8], and UBERON [9]. | ||
| * E.5 IRI for OcIMIDo is: https://github.com/sap218/ocimido/blob/master/ontology/ocimido.owl#OCIMIDO_00000. | ||
| * E.6 Identifier generation policy: Protégé’s preferences schema is that ontology’s entities are to have the prefix “OCIMIDO” followed by an underscore then a five digit number: currently they consists of 00001 up to ~000600. All classes have OCIMIDO prefix and own numeric identifier since OcIMIDo avoids importing axioms from other ontologies. | ||
| * E.7 Entity metadata policy: currently `exact` synonyms in the ontology are additional clinical/medical terms. However `broad` synonyms are to be used for all Layman terms from the tf-idf method extracting from [Olivia's Vision](http://www.oliviasvision.org/) open forum. | ||
| * E.8 BFO [10] and RO [11] were used as upper ontologies. | ||
| * E.9 Currently, relationships in OcIMIDo are cross-referenced, such as `adjacent to` and `treatment of` from RO. We defined our own, `investigated by` (inverse `investigation for`) based on the investgations from the medical document [3]. | ||
| * E.10 Axiom patterns are inferred from the ontology structure itself (`subclass`) and by defined relationships, `is a` - currently only 100% true cases. | ||
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| **F Managing change** | ||
| * F.1 Sustainability plan: OcIMIDo is freely available on GitHub and the creator, Samantha C Pendleton, will constantly update/change based on expert opinion or via Issue notifications. Anyone from the community can suggest new terms, but with sufficient evidence/justification. Potentially users can `fork` the ontology and make their own changes, which then allows the creator to merge these changes. If often particular individuals are making positive/appropriate changes they can be given direct access to co-maintain the ontology with the creator. | ||
| * F.2 There is the change log ([CHANGELOG.md](https://github.com/sap218/ocimido/blob/master/CHANGELOG.md)) for entitles which need to be removed/split/redefined, additionally we can annotate these entities as obsolete. | ||
| * F.3 Ontology will follow “semantic versioning” guidelines and that it will maintain as version 1 unless a major foundation change is made then it will become version 2. Otherwise additional terms/fixes will increment to version 1.1 or 1.0.1 over time. | ||
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| **G Quality Assurance** | ||
| * G.1 Successful testing on the Olivia’s Vision public forum for the `broad` synonyms plus annotations. Also used Protégé’s Pellet reasoner to ensure a coherent and consistent ontology. Experts in the opthamology background deemed/judged the ontology achieves the claims. | ||
| * G.2 Ontology is novel and first in ophthalmology. Additionally this method of building (tf-idf) is validated and proven a fast approach to synonym curation. OcIMIDo meets the stated requirements as an ontology suitable for the opthamology domain in additon to capturing the "patient voice. | ||
| * G.3 An example of application is using the broad synonyms/Layman terms for sentiment analysis on the Olivia's Vision forum. Additionally future applications include GWAS/phenotype analysis on the UK Biobank cohort and other electronic health databases - OcIMIDo provides an implicit axiomatic structure for data annotated with SNOMED-CT, ICD-10, ICD-9, or Read codes as these are included as cross-references in the ontology, enhancing the potential value of OcIMIDo for searching and curating unstructured clinical data. | ||
| * G.4 Ontology not yet available on OBO Foundry or other public repositories. However freely available on GitHub - ask creator if you wish for an alternative ontology format. | ||
| 5) G.5 Evidence of use* (MUST): An illustration of active projects and applications that use the ontology. | ||
| ◦ Current evidence of OcIMIDo application is sentiment analysis on the Olivia’s Vision forum using the terms and synonyms for annotations, **note**: as soon as the manuscript is accepted the creator will include a reference/link here. | ||
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| **Requirements / Development Community** | ||
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| *Contributors* | ||
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| * Luke T Slater | ||
| * Alastair K Denniston | ||
| * Georgios V Gkoutos | ||
| [1] Matentzoglu, N., Malone, J., Mungall, C., & Stevens, R. (2018). MIRO: guidelines for minimum information for the reporting of an ontology. Journal of Biomedical Semantics, 9(1), 6. | ||
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| * See :grey_exclamation: [Issues](https://github.com/sap218/ocular-immune-mediated-inflammatory-disease-ontology/issues) for the term-tracker if user wants to submit a request (new term/change/suggestion) - if frequent issues when an additional main contributor will be added | ||
| [2] Dean, S., Mathers, J. M., Calvert, M., Kyte, D. G., Conroy, D., Folkard, A., Southworth, S., Murray, P. I., & Denniston, A. K. (2017). “The patient is speaking”: discovering the patient voice in ophthalmology. The British Journal of Ophthalmology, 101(6), 700–708. | ||
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| **Knowledge Acquisition** | ||
| [3] Denniston, A. K., Lee, R. W., Pavesio, C., Stanford, M. R., Murray, P. I., Okada, A., Sen, H. N., & Dick, A. D. (2018). Uveitis Dataset Clinical Dataset. The Royal College of Ophthalmologists. https://www.rcophth.ac.uk/wp-content/uploads/2014/12/Uveitis-Data-Set-Oct-2018.pdf | ||
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| * an expert derived ontology | ||
| * used other biomedical ontologies from online repositories | ||
| * foundation based on [RCOphth](https://www.rcophth.ac.uk/wp-content/uploads/2014/12/Uveitis-Data-Set-Oct-2018.pdf) | ||
| * layman's terms based on [OV](http://www.oliviasvision.org/) | ||
| [4] Côté, R. G., Jones, P., Apweiler, R., & Hermjakob, H. (2006). The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics, 7, 97. | ||
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| [5] Schriml, L. M., Arze, C., Nadendla, S., Chang, Y.-W. W., Mazaitis, M., Felix, V., Feng, G., & Kibbe, W. A. (2012). Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Research, 40(Database issue), D940–D946. | ||
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| **Ontology Content** | ||
| [6] Robinson, P. N., Köhler, S., Bauer, S., Seelow, D., Horn, D., & Mundlos, S. (2008). The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. American Journal of Human Genetics, 83(5), 610–615. | ||
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| * `IRI`s: https://github.com/sap218/ocimido/blob/master/ontology/ocimido.owl#OCIMIDO_00001 | ||
| [7] Vasant, D., Chanas, L., Malone, J., Hanauer, M., Olry, A., Jupp, S., Robinson, P. N., Parkinson, H., & Rath, A. (2014). Ordo: An ontology connecting rare disease, epidemiology and genetic data. Proceedings of ISMB, 30. | ||
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| * 615 classes, with 210 of those extracted from the [RCOphth](https://www.rcophth.ac.uk/wp-content/uploads/2014/12/Uveitis-Data-Set-Oct-2018.pdf) and 234 expert opinion | ||
| * entities/concepts are `OCIMIDO` - not to be confused w/ ontology abbreviation: OcIMIDo | ||
| * 1567 relationships (including axioms) | ||
| * 2600 annotations with those 948 being xrefs (570 to medical ontologies which of those 363 xrefs to SNOMED-CT) | ||
| * and a total of 131 synonyms from [OV](http://www.oliviasvision.org/) | ||
| [8] Gkoutos, G. V., Schofield, P. N., & Hoehndorf, R. (2018). The anatomy of phenotype ontologies: principles, properties and applications. Briefings in Bioinformatics, 19(5), 1008–1021. | ||
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| * OWL/XML Syntax w/ `Protégé` | ||
| * used `Protégé’s` `Pellet` reasoner which resulted in a coherent and consistent ontology | ||
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| * ontologies cross-references: `DOID`, `HPO`, `ORDO`, `PATO`, `UBERON`, `ICD-10`, `Read Codes`, `SNOMED-CT` | ||
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| * relationships (not including inverses): `adjacent to`, `part of`, `characterised by`, `investigated by`, `is a`, `occurs in`, `treatment of` | ||
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| * metadata/annotations: `rdfs:comment`, `rdfs:databaseCrossReference`, `rdfs:extractedFrom`, `rdfs:hasExactSynonym`, `rdfs:synonymExtraction` | ||
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| [9] Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., & Haendel, M. A. (2012). Uberon, an integrative multi-species anatomy ontology. Genome Biology, 13(1), R5. | ||
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| Following the MIRO guidelines for reporting on an ontology [1] - additional content will be included in the OcIMIDo paper | ||
| [10] Smith, B., Kumar, A., & Bittner, T. (2005). Basic Formal Ontology for Bioinformatics. IFOMIS Reports. | ||
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| [1] Matentzoglu, N., Malone, J., Mungall, C. and Stevens, R., 2018. MIRO: guidelines for minimum information for the reporting of an ontology. *Journal of biomedical semantics*, 9(1), p.6. accessed via: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0172-7 | ||
| [11] Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A. L., & Rosse, C. (2005). Relations in biomedical ontologies. Genome Biology, 6(5), R46. |