Ontology Lookup Service (OLS)

1. Resource facilitation to scientific research

a. Interoperability Resource: Briefly describe the function of the Interoperability Resource

OLS provides integrated services for accessing/visualising biomedical ontologies. OLS includes a user interface for search in single or multiple ontologies. Browsing ontologies as trees or as node-edge diagrams is supported. The RESTful API provides a unified way to access ontologies programmatically. OLS is used to map data as text annotations to ontologies and embeds access to ontologies in curation interfaces or in high-throughput data annotation pipelines that automatically map and validate data to ontologies. It is by used several ELIXIR Core Data Resources and Core Data Deposition Databases and is core to delivering semantic interoperability for FAIR data access.

b. Scope statement: describe the scope , and the users of the resource. How is the Interoperability Resource positioned with respect to other similar Interoperability Resources ? Include the base URL and, if relevant, the introductory or “about” page URL.

The OLS provides web based and API search over 200 highly accessed public biomedical ontologies. OLS acts as a hub for accessing ontologies and is a critical service infrastructure for building interoperable data in the life sciences supporting the ‘i’ of FAIR. OLS is used by a range of users including ontology builders, data curators, and bioinformaticians who are integrating ontologies into applications and data curation pipelines. OLS is dedicated to serving open access ontologies conforming to OBO or OWL standards. The content is curated by the EBI to ensure quality and relevance of content to the community and ontologies can be extended by request. OLS interoperates with ELIXIR data resources and international projects and other interoperability services, for example, OLS conforms to identifier standards by providing a compact id resolution service for ontology terms that has been harmonised with identifiers.org. OLS uses API standards (REST+HAL) and supports ELIXIR metadata activities by conforming to minimal metadata about ontologies as defined by OBO Foundry. OLS is used within ELIXIR platforms, for example by the tools platform, the Human Data Platform and Interoperability platform. OLS has unique features, such as the OxO service and integrated Zooma services providing unique tools for mapping between ontologies and mapping text to ontologies for both archival and added value resources. OLS has developed schema.org markup for all 6 million ontology term pages in compliance with BioSchemas and a standard for describing ontology annotations was developed and deployed in over 5 million BioSamples pages.

c. Resource url

https://www.ebi.ac.uk/ols/

d. Inter-organisational recognition: does the Interoperability Resource have community recognition? (e.g. demonstrated through a collaboration, geographical diversity in the source of the submissions, international diversity of delivery partners and/or funders)

OLS is one of two highly accessed major international services delivering ontologies to the biomedical community (the other is BioPortal). OLS is a major international interoperability service and is the default resolver for many internationally developed and accessed ontologies (e.g. Evidence Code Ontology, Sequence Ontology (SO), Experimental Factor Ontology). OLS also hosts all of the Open Biomedical Ontology library and updates nightly to ensure the latest versions of all ontologies are available to our users. OLS usage by country lists the United State, United Kingdom, Germany, India and China as the top 5 countries with request from 164 countries in total with ~40% of our overall usage coming from European countries. OLS collaborates with industry (e.g. Pistoia Alliance), is dockerised for cloud portability and running in several Pharma/Agrifood companies including GSK. OLS’s user community is international and is funded by two EC grants, one IMI grant (in negotiation), OpenTargets (Industrial/Academic precompetitive Consortium) and EMBL-EBI funds. OLS is used by other infrastructures and is funded in part by the CORBEL EC award. This allows us to extend the tool suite to support new domains, such as Marine Biology and BioBanks. Other collaborations include GA4GH were OLS is represented in the Clinical and Phenotype Working group.

2. Community

a. Community impact: If applicable, provide documented evidence of community impact (e.g., publication citations, API calls, projects using the resource, etc.)

OLS averages 8,000 unique visitors to the site each month and receives over 40 million requests to the website or API combined per month.
OLS is integral to the release process for many data resource such as Expression Atlas, Human Cell Atlas, PRIDE, EVA, The GWAS Catalog and OpenTargets and is also used by the biocuration community to map annotation to ontology terms
OLS a major community request base and has a process and resource to make service changes based on community use cases. Examples of ELIXIR communities engaged include e.g. tools platform, interoperability platform and Human Data
OLS ontology changes allowing users to detect rarely updated ontologies and to determine rate of ontology evolution, this is an importance metric of quality and can also be used by ontology developers to review changes.
OLS supports community activities such as OBO Foundry, FAIR data and is represented in OBO Foundry by Simon Jupp and Melanie Courtot, ensuring OLS can evolve based on community need. 
OLS supports community formats such as OBO and OWL and as ELIXIR standards become available
OLS innovates to extend the services around OLS, for example the Ontology cross Reference (OxO) Service was built with Pistoia Alliance collaboration to map disease and phenotype ontologies by consuming OLS’s services.

b. Potential usage: Describe other systems that could use this candidate resource, but currently do not.

We are able to extend the range of ontologies within OLS to support new communities in generating and serving their ontologies e.g. H3Africa Sickle Cell and Human Cell Atlas. There is no biomedical domain specificity in OLS and we have engaged with communities such as EUDAT and the Research Data Alliance (RDA) Vocabulary to promote our services. We also work closely with Pharma, Agrifood and SMEs who wish to access or serve ontologies. Licensing restrictions for health based ontologies such as SNOMED-CT mean we are unable to serve these directly and we therefore have developed the OxO service to allow translation to-and-from these. This allows us to work in the translational space driving the ELIXIR Human Data community and with GA4GH. By ensuring our toolset is portable we are able to support scenarios where data must be locally hosted, for example data stored in a Local EGA instance.

c. Outreach & support: Provide resource support publication(s)/user documentation(s) describing the Interoperability Resource (e.g. scientific journal publications, community preprints, resource user’s documentations etc.), resource dissemination plan (e.g. workshops, conference presentations), and other equal-opportunity research support (if applicable).

The OLS team has a training remit both for academic users (via ELIXIR, TeSS,EMBL-EBI courses, for specific projects) and industrial users via EMBL-EBI’s industry programme and direct industry engagement. Our materials are widely shared and an Apache 2.0 licence promotes community reuse. Our training strategy is supported by EMBL-EBI’s and ELIXIR’s training activities and in addition we benefit from these organisations dissemination tools and personnel, such as the ELIXIR interoperability Coordination activities.

* Video training/presentation: https://www.youtube.com/watch?v=p8XF7yJvW4E, https://www.youtube.com/watch?v=p8XF7yJvW4E

* Recent Workshop and training materials https://www.ebi.ac.uk/spot/Workshops/ 
* Online training on ontologies https://www.ebi.ac.uk/training/online/course/ontology-lookup-service-ol…;

* OLS API documentation https://www.ebi.ac.uk/ols/docs/index 

* Source code and documentation https://github.com/EBISPOT/OLS 
* TeSS https://tess.elixir-europe.org/materials/ontology-lookup-service-ols)

Publications

* Côté RG, Jones P, Apweiler R, Hermjakob H. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics. 2006;7 97. doi:10.1186/1471-2105-7-97. PMID: 16507094; PMCID: PMC1420335. Cited 66 times

* Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H. The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res. 2008 Jul;36(Web Server issue) W372-6. doi:10.1093/nar/gkn252. PMID: 18467421; PMCID: PMC2447739. Cited 33 times.

* Perez‐Riverol Y, Ternent T, Koch M, et al. OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets. Proteomics. 2017;17(19):1700244. doi:10.1002/pmic.201700244.

d. Dependency of other resources: How is this resource critical to the user(s)? Do other resources depend on the resource described here to provide downstream service? Please list, or provide a link to a diagram.

OLS is used throughout the data archiving, standards compliance, data curation, and added value resource production process for many ELIXIR, international and industrial resources. Examples are shown in Table 1. OLS papers are cited 159 times and Ontologies hosted by OLS that are critical to ELIXIR activities and services include: ORDO (Rare Disease), EDAM (Tools and Training Platforms), DUO (Human Data Community, GA4GH).

Details of dependencies to specific resources are listed here https://github.com/EBISPOT/ebispot.github.io/blob/master/ols-dependenci…

3. Quality of resource

a. Uptime: Average percentage uptime/month during the last 12 months, response time of the resource. In case of ontology/standards production, interval of update/release, adaptability of ontology design patterns to evolving data. Provide information where applicable: uptime of resource, software release cycle (please state week/month etc), update frequency.

OLS is hosted in EMBL-EBI’s data centres with load balancing, failover and has >99% uptime as monitored by https://uptimerobot.com. 

Response time recorded with https://tools.pingdom.com/ . 

https://www.ebi.ac.uk/ols/ homepage: Load time in seconds
Sweden - 1.24 s 
North America - 3.7 s
Australia - 6.2 s

Typical search for e.g. diabetes https://www.ebi.ac.uk/ols/search?diabetes, load time in seconds
Sweden - 0.64 s 
North America - 3.5 s
Australia - 4.0 s

OLS development is agile, in response to community requests submitted via an open tracker (https://github.com/EBISPOT/OLS/issues), support is provided to users by mailing list “ols-support@ebi.ac.uk” and an announce list alerts users to new releases “https://listserver.ebi.ac.uk/mailman/listinfo/ols-announce”. OLS complies with sustainable SW development practices (many of which overlap with this document) i.e. has a clear licence Apache 2.0, uses open source development frameworks, has clear support and documentation encouraging community feedback and contribution. The project has been running since 2008, most recently it was redeveloped in 2016 and usage has doubled in that time as has the sustainability of the project as the codebase was improved. Most recently OLS was dockerised for community use. Each ontology is checked for new versions nightly and these are loaded for access immediately, ensuring latest versions are available for community.

b. Accessibility: what are resource retrieval mechanisms? Does the resource provide web-based user interface, application programmable interface (API), containers, and/or other channels? Please list resource access mechanism, provide URLs as applicable.

OLS has a GUI designed using UX practices with community feedback providing search, browse and ontology graph visualisation and a RESTful API:

* Web interface https://www.ebi.ac.uk/ols/
* RESTful API https://www.ebi.ac.uk/ols/docs/api
* Supported formats JSON, JSON-HAL, XML, RDF, CSV
* SPARQL endpoint https://www.ebi.ac.uk/rdf/services/sparql 
* Docker container https://hub.docker.com/r/ebispot/ols/ 
* Java API https://github.com/EBISPOT/ols-client 
* Ontology supported formats OWL/OBO

c. Maintenance quality: Is there a maintenance SOP or plan, reflecting sustainability and scalability? Does it align with guidelines for sustainable software development? Please include a resource commitment statement (description text or URL).

OLS is developed with industry grade software ranging from the backend databases that are provided by MongoDB, Neo4j and Apache Solr to the Java based Web service framework that is built using Spring Data. These are technologies that are well supported with large developer communities and have been shown to be reliable and scalable in a number of industry settings. We are committed to the open source development of these tools under the EMBL-EBI terms of use and all source code is provided under a Apache 2.0 licence. We have a well documented build and deploy process and deliver both the software and data for OLS using industry standard continuous integration and deployment software Bamboo, provided by Atlassian. We’ve recently containerised the OLS software with Docker to allow for deployment in different settings and have live instances of OLS running in Amazon Web Services. OLS has been hosted by EMBL-EBI for more than 10 years and is actively developed with a major update in 2016. The EMBL-EBI virtualised infrastructure provides resilience for the service by hosting it in a number of data centres with appropriate fallback and failover mechanisms and by load-balancing requests across data centres we are able to scale the service in response to user demand.mbedded and sustained by a portfolio of research and infrastructure projects awarded to Prof. Sansone, including funds from the NIH Data Commons.

d. Support quality: Please list support mechanisms (e.g., point of contact, request ticketing, resource’s response time where a solution is identified, etc.), and methods to collect user feedback. If available, list tutorial documentations or tutorial materials and format, including linking on the ELIXIR’s Training Portal (TeSS) (or other training platforms) where applicable.

* Public support issue tracker ols-support@ebi.ac.uk - response time 24 hours
* GitHub issue tracker https://github.com/EBISPOT/OLS/issues
* Public announcement mailing list https://listserver.ebi.ac.uk/mailman/listinfo/ols-announce 
* Twitter feed https://twitter.com/ebiols 
* Video training/presentation: https://www.youtube.com/watch?v=p8XF7yJvW4E, https://www.youtube.com/watch?v=p8XF7yJvW4E
* Recent Workshop and training materials https://www.ebi.ac.uk/spot/Workshops/ 
* Online training onontologies https://www.ebi.ac.uk/training/online/course/ontology-lookup-service-ol…;
* OLS API documentation https://www.ebi.ac.uk/ols/docs/index 
* Source code and documentation https://github.com/EBISPOT/OLS

4. Legal framework, funding, and governance

a. Legal framework: What are the resource’s license/terms of use? Can the license facilitate Open Science? Please include the url for the license the resource uses.

EMBL-EBI is committed to OpenScience through its mission to provide freely available online services, databases and software relating to data contributed from life science experiments to the largest possible community. OLS is available under EMBL-EBI’s standard terms of use and all code is in an open git repository under EMBL-EBI’s Apache 2.0 licence. The development strategy for the resource includes a commitment to portable software and use of public open source libraries documented here: https://www.ebi.ac.uk/ols/docs/about

Compliant with EMBL-EBI Privacy Policy (http://www.ebi.ac.uk/about/terms-of-use) and compliant with EMBL-EBI’s GDPR processes for the service, related lists and activities.

b. Privacy/Ethics policy: If applicable, is there a publicly available privacy policy in which use and security around personal data are described (e.g. the EU General Data Protection Regulation (GDPR), ELIXIR Ethics Policy, other relevant ELIXIR Policies)? Please include the url of the privacy/ethics policy, if applicable.

EMBL’s is an international organisation and the privacy policy is described here https://www.embl.de/aboutus/privacy_policy/
EMBL-EBI has a site wide GDPR process for our services, tools and activities collecting personal data. OLS therefore has GDPR notices compliant with process using a consent based model. On changes to the service we review and revise the notices as needed and EMBL’s Data Protection Officer provides advice on GDPR Implementation for all EBI services.

OLS privacy notice for public website
https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-we…;

OLS privacy notice for submitting new ontologies https://www.ebi.ac.uk/data-protection/privacy-notice/ols 

OLS privacy notice for mailing lists https://www.ebi.ac.uk/data-protection/privacy-notice/ols-mailing-list

c. Funding & sustainability plan: List of funding sources supporting the resource, and sustainability plan.

OLS has been hosted at EMBL-EBI for >10 years. EMBL-EBI and external funds have been used during this period to maintain/extend the service. OLS is currently funded by: EMBL-EBI core funds and OpenTargets EBI-OT01 (OTAR005), EC CORBEL (EC/H2020-654248), ELIXIR EXCELERATE (EC/H2020-676559), OpenTargets (OTAR005, OTAR009, OTAR017, OTAR02-046-02) and the Human Cell Atlas (CZI 2017-171304). Most recently we have been awarded an IMI FAIR data grant which will, in part, fund OLS till 2021. We therefore expect to maintain OLS with grant and internal funding, a model which has been successful for EMBL-EBI’s Molecular Archive cluster for >30 years.

d. Governance: Describe the Resource’s QA/QC plan that guarantees similar quality governance to that of ELIXIR. Please link SAB members, if applicable.

OLS is a service of the EMBL-EBI Samples, Phenotypes and Ontologies Team led by Helen Parkinson. Simon Jupp is the team’s dedicated Ontology Project Lead and has worked delivering semantic services and ontologies for more than 10 years. EMBL-EBI Team Leaders are reviewed on a four yearly cycle based on the quality of the services delivered, OLS is included in this process. The last review was in 2015 (rating: outstanding), the next review is due in 2019. Additionally, the OLS is advised by an annual Scientific Advisory Board, currently comprising: Lee Harland (Chair, SciBite), Mario Caccamo (NIAB), Maryann Martone (UCSF), Robert Stevens (Manchester) and Carol Hamilton (RTI). The SAB membership rotates every 3 years and ELIXIR Hub leadership are also invited to each Scientific Advisory Board Meeting as observers. The grants that fund OLS are peer reviewed at the point of submission, and undergo periodic review during the funding cycle. For example, the CORBEL EC grant is a current funder of OLS, Parkinson is the Interoperability Work Package (WP6) co-lead and WP6 (including OLS) received an excellent review. Given the mixed funding model, we expect these mechanisms, plus critical feedback and requests from our diverse and large user community, to enable us to continue to provide OLS as a high quality, highly accessed resource.