DiSSCo Prepare Milestone report MS5.5 - Compilation of relevant data standards

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Title DiSSCo Prepare Milestone Report MS5.5 "Compilation of relevant data standards" Author(s) Petersen, Mareike von Mering, Sabine Glöckler, Falko Identifier of the author(s) https://orcid.org/0000-0001-8666-1931 (MP) https://orcid.org/0000-0003-2982-7792 (SvM) https://orcid.org/0000-0002-7127-2738 (FG) Affiliation Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science (https://ror.org/052d1a351) Contributors Addink, Wouter Hardisty, Alex Abarenkov, Kessy Fichtmüller, David Publisher Identifier of the publisher Resource ID https://doi.org/10.34960/3mg1-7n14 Publication year 2021 Related identifiers Is it the first time you submit this outcome? Yes Creation date 15/01/2021 Version 1 Citation Petersen, M., von Mering, S. & Glöckler, F. 2021: DiSSCo Prepare Milestone Report MS5.5 "Compilation of relevant data standards”. https://doi.org/10.34960/3mg1-7n14 Abstract This Milestone Report covers data standards and ontologies relevant for the DiSSCo research infrastructure. Together with other project outputs of DiSSCo Prepare this report is identifying and documenting important building blocks for the technical Infrastructure of DiSSCo. The compilation will be available via the currently developed DiSSCo Knowledgebase. Content keywords scientific Project reference DiSSCo Prepare (GA-871043) WP number WP5 Project output Milestone report Deliverable/milestone number MS5.5 Dissemination level Public Rights License CC0 1.0 Universal (CC0 1.0) Resource type Text Format PDF Funding Programme H2020-INFRADEV-2019-2 Contact email [email protected] 36 DiSSCo Prepare WP 5 Common Resources and Standards – MS 5.5 Compilation of relevant data standards WP Lead: Mareike Petersen (MfN) Task Lead: Mareike Petersen & Falko Glöckler (both MfN) Authors: Mareike Petersen, Sabine von Mering & Falko Glöckler (all MfN) Contributors: Kessy Abarenkov (Tartu), Wouter Addink (Naturalis), David Fichtmüller (BGBM), Alex Hardisty (Cardiff) 2 Abstract Key words This Milestone Report covers data standards and ontologies relevant for the DiSSCo research infrastructure. Together with other project outputs of DiSSCo Prepare this report is identifying and documenting important building blocks for the technical Infrastructure of DiSSCo. The compilation will be available via the currently developed DiSSCo Knowledgebase. Knowledgebase, ontology, data standard Grant Agreement number: 871043 — DiSSCo Prepare — H2020-INFRADEV-2018-2020 / H2020-INFRADEV-2019-2 3 INDEX 01 INTRODUCTION 5 02 APPROACH 5 03 RESULTS 6 Data Standards 6 a. Standards relevant for the description of specimen and Bioand Geodiversity 6 Access to Biological Collection Data 6 Access to Biological Collection Data Extension for Geosciences 7 CETAF Specimen Preview Profile Fehler! Textmarke nicht definiert. Darwin Core 8 Ecological Metadata Language 8 Extended Specimen Concept 9 Humboldt Core 9 Open Digital Specimen 10 Taxonomic Concept Transfer Schema 10 b. Standards relevant for the description of collections 11 Collection Description Standard 11 Minimum Information about a Digital Specimen 11 c. Standards relevant for the description of tissues and sequences 12 Global Genome Biodiversity Network Data Standard 12 Minimum Information about any (x) Sequence 12 d. Standards relevant for the description of digital multimedia assets 13 Audubon Core 13 e. Standards related to localities 13 Geography Markup Language 13 ISO 3166 – 1 14 4 ISO 3166 – 2 14 f. Other relevant standards 15 Ecological Trait-data standard 15 Bioschemas.org 15 CloudEvents 16 Data Quality Vocabulary 16 Datacite Metadata Schema 17 Digital Object Interface Protocol 17 FAIR Digital Object Framework 18 FAIR Implementation Profile 18 Schema.org 19 Structured Descriptive Data 19 W3C PROV 20 Web Annotation Data Model 20 Ontologies 21 PROV-O 21 Biological Collections Ontology 21 Ontology for Biomedical Investigations 21 Information Artifact Ontology 22 Open Digital Specimen Ontology 22 MarineTLO ontology 22 04 OUTLOOK 23 5 01 INTRODUCTION DiSSCo Prepare will build on profound technical knowledge from various sources and initiatives. In order to allow for efficient knowledge and technology transfer for partners building the DiSSCo technical backbone, a central and freely-accessible DiSSCo Knowledgebase will be designed and implemented. The knowledgebase will include structured technical documentation of identified DiSSCo technical building blocks, an assessment of their technical readiness for DiSSCo, as well as specifications on their relevance for the overall DiSSCo technical infrastructure and the DiSSCo data model. In this first Milestone Report linked to the Knowledgebase development we compile a list of relevant data standards and ontologies for bioand geo-collection objects, collection descriptions, and digital assets. Relevant Persistent Identifier (PID) Systems are in focus of MS 5.3 “Documentation of PIDs relevant for DiSSCo technical infrastructure” due in Month 18 and are not part of this Report. Data standards are the rules by which data are described and recorded. In order to share, exchange, and understand data, we must standardize the format as well as the meaning 1 . Ontologies are usually domain specific and describe categories properties and relations between concepts, data, or entities. The compilation will be available via the DiSSCo Knowledgebase (currently under development). This list of standards and further building blocks to be prepared will be an important reference for DiSSCo Preparatory Phase (DPP) project partners, tasks within the project as well as tasks and developments in other DiSSCo related projects (e.g. Helpdesk developed under Synthesys+). 02 APPROACH Relevant building blocks were collected from known organizations coping with the standardization, publication and exchange of data related bioand geodiversity and beyond. Especially important for the development of standards in our domain is Biodiversity Information Standards (TDWG). This not-for-profit, scientific and educational association was formed to establish international collaboration among the creators, managers and users of biodiversity information and to promote the wider and more effective dissemination and sharing of knowledge about biological organisms. The TDWG community develops, ratifies and promotes standards and guidelines for the recording and exchange of data about organisms and brings together experts/specialists in different TDWG Interest and Task Groups working on specific topics and standards. Other important organizations with respect to relevant outputs are the Research Data Alliance and the World Wide Web Consortium. The Research Data Alliance (RDA) is a communitydriven international initiative with the goal of sharing and re-use of data by building the technical but also societal infrastructure. It can be defined by its vision: “Researchers and innovators openly share and re-use data across technologies, disciplines, and countries to address the grand challenges of society.” and mission: “RDA builds the social and technical bridges that 1 U.S. Geological Survey: Data Standards: https://www.usgs.gov/products/data-and-tools/data-management/datastandards#:~:text=Data%20standards%20are%20the%20rules,as%20well%20as%20the%20meaning 6 enable open sharing and re-use of data.” Many of the RDA recommendations and developments will be part of the data lifecycle in DiSSCo 2 . The World Wide Web Consortium (W3C) is an international community where Member organizations, a full-time staff, and the public work together to develop Web standards. The W3C mission is to lead the World Wide Web to its full potential by developing protocols and guidelines that ensure the long-term growth of the Web 3 . 03 RESULTS Data Standards Data standards were collected from relevant sources in a tabular format including information on Name, Focus, Status, Maintenance, Documentation, Citation, and Further reading. The standards are grouped according to their field of application. In each subsection the standards are in alphabetical order. Although the list is already very comprehensive, further standards might be of interest or relevance during ongoing development of the DiSSCo Research Infrastructure. a. Standards relevant for the description of specimen and Bioand Geodiversity Name Access to Biological Collection Data Focus The Access to Biological Collection Data (ABCD) Schema is an evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data). Use cases are e.g. GBIF, GFBio, Europeana. Maintenance TDWG current (2005) standard (Version 2.06), a new version (3.0) is already available but not yet ratified by TDWG; maintained by the ABCD Maintenance Group Documentation https://github.com/tdwg/abcd/ https://abcd.tdwg.org/terms/ Citation Access to Biological Collection Data task group. 2007. Access to Biological Collection Data (ABCD), Version 2.06. Biodiversity Information Standards (TDWG) http://www.tdwg.org/standards/115 Further reading ABCD 3.0 is the new version of the standard Fichtmüller D, Berendsohn W, Droege G, Glöckler F, Güntsch A, Hoffmann J, Holetschek J, Petersen M, Reimeier F (2019) ABCD 3.0 Ready to Use. Biodiversity Information Science and Standards 3: e37214. https://doi.org/10.3897/biss.3.37214 2 Islam S, Hardisty A, Addink W, Weiland C and Glöckler F (2020) Incorporating RDA Outputs in the Design of a European Research Infrastructure for Natural Science Collections. Data Science Journal, 19(1), p.50. DOI: http://doi.org/10.5334/dsj-2020-050 3 World Wide Web Consortium: https://www.w3.org/Consortium/ 7 Name Access to Biological Collection Data Extension for Geosciences Focus Extension for Geosciences (EFG) extends the ABCD schema to integrate geological data, including information about paleontological and geological collection items. Use cases are e.g. GeoCASe Portal, Europeana. Maintenance Since March 2017 under ratification by TDWG, maintained by the TDWG EFG Task Group Documentation https://github.com/tdwg/efg Citation Original Citation: Kiessling W, Rissoné A, Copp C, Döring M, Mewis H (2006): The EFG extension to the ABCD schema Further reading Petersen M, Glöckler F, Kiessling W, Döring M, Fichtmüller D, Laphakorn L, Baltruschat B, Hoffmann J (2018). History and development of ABCDEFG: a data standard for geosciences. Fossil Record, 21(1), 47-53. https://doi.org/10.5194/fr-21-47-2018 Name CETAF Specimen Preview Profile Focus The CETAF Specimen Preview Profile (CSPP) is a minimal set of agreed (RDF) collection metadata elements implemented consistently across CETAF (Consortium of European Taxonomic Facilities) organisations. The purpose of CSPP is to provide a stable resource enabling preview functions in specimen portals. The CSPP is not meant to be comprehensive, which means that Linked Open (collection) Data implementations of CETAF institutions will usually provide much richer metadata with additional RDF-elements. Use case e.g. CETAF/JACQ Botany Pilot (https://services.bgbm.org/botanypilot/person/q/Q1349394). Maintenance CETAF ISTC (Information Science & Technology Commission); actively supported by many CETAF institutions, more to come Documentation https://cetafidentifiers.biowikifarm.net/wiki/CETAF_Specimen_Preview_P rofile_(CSPP) Citation - Further reading https://cetafidentifiers.biowikifarm.net/wiki/Questions,_problem_solutions _and_further_discussions_(Guide_of_best_practices)#CETAF_Specimen _Preview_Profile_.28CSPP.29 14 Name ISO 3166 – 1 Focus Codes for the representation of names of countries and their subdivisions – Part 1: Country code. Standard defining codes for the names of countries, dependent territories, and special areas of geographical interest Maintenance International Organization for Standardization (ISO) Documentation https://isotc.iso.org/livelink/livelink?func=ll&objId=16944257 Citation Further reading https://www.iso.org/iso-3166-country-codes.html Name ISO 3166 – 2 Focus Codes for the representation of names of countries and their subdivisions – Part 2: Country subdivision code. Standard defining codes for country subdivisions (administrative territorial entity). Usually only the top levels of a country are assigned ISO 3166-2 codes, but sometimes there is a second level hierarchy. Maintenance International Organization for Standardization (ISO), actively maintained (2-4 updates a year) Documentation https://www.iso.org/obp/ui/#iso:std:iso:3166:-2:ed-4:v1:en Subdivisions of an individual country can be viewed using the ISO Online Browsing Platform with the ISO 3166-1 alpha 2 country code: https://www.iso.org/obp/ui/#iso:code:3166:<code> , e.g. https://www.iso.org/obp/ui/#iso:code:3166:DE Citation Current Version: ISO 3166-2:2020(en) Codes for the representation of names of countries and their subdivisions — Part 2: Country subdivision code, Committee: ISO/TC 46, Edition: 4, Publication date: 2020-08, ICS: 01.140.30. Further reading https://en.wikipedia.org/wiki/ISO_3166-2 (note that the lists provided by Wikipedia and Wikidata are in some cases outdated) 15 f. Other relevant standards Name Ecological Trait-data standard Focus This defined vocabulary aims at providing all essential terms to describe datasets of functional trait measurements and facts for ecological research. Use case e.g. GFBio (German Federation for Biological Data) Maintenance ETS Vocabulary is under continuous and open community development, hosted on GitHub. It has been ported to the GFBio Terminology Service. Documentation https://terminologies.gfbio.org/terms/ets/pages/ Citation Schneider FD, Jochum M, Provost GL, Ostrowski A, Penone C, Fichtmüller D, Güntsch A, Gossner MM, König-Ries B, Manning P, Simons NK (2019). Towards an Ecological Trait-data Standard, Methods in Ecology and Evolution, 10:2006-2019 Further reading https://github.com/EcologicalTraitData/ETS Name Bioschemas.org Focus Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Use case e.g. MNHN Paris, see also https://bioschemas.org/liveDeploys/ Maintenance different types and profiles of the standard are maintained by different groups, active community Documentation https://bioschemas.org/types/ https://bioschemas.org/profiles/ Citation https://bioschemas.org Gray AJG, Goble CA and Jimenez R (2017) Bioschemas: From Potato Salad to Protein Annotation. In International Semantic Web Conference (Posters, Demos & Industry Tracks)." Further reading https://bioschemas.org/ https://github.com/BioSchemas/specifications 16 Name CloudEvents Focus CloudEvents is a specification for describing event data in common formats to provide interoperability across services, platforms and systems. CloudEvents has received a large amount of industry interest, ranging from major cloud providers to popular SaaS companies. Approved as a Cloud Native sandbox level project on May 15, 2018 Maintenance hosted by the Cloud Native Computing Foundation (CNCF), actively developed Documentation https://github.com/cloudevents Citation Further reading https://cloudevents.io/ Name Data Quality Vocabulary Focus “The Data Quality Vocabulary (DQV) provides a metadata model for expressing data quality. DQV was developed by the Data on the Web Best Practice (DWBP) Working Group of the World Wide Web Consortium (W3C) between 2013 and 2017.” Maintenance W3C Working Group Note 15 December 2016, maintained by the Data on the Web Best Practice (DWBP) Working Group of the W3C Documentation https://www.w3.org/TR/vocab-dqv/ Citation Albertoni R and Isaac A (2021) Introducing the Data Quality Vocabulary (DQV)’. Semantic Web, Volume 12, 1 Jan. 2021 : 81 – 97. https://doi.org/10.3233/SW-200382 Further reading https://github.com/w3c/dwbp 17 Name Datacite Metadata Schema Focus The DataCite Metadata Schema is a list of core metadata properties chosen for an accurate and consistent identification of a resource for citation and retrieval purposes, along with recommended use instructions. It is used for DOI creation for research data via DataCite. Maintenance DataCite Metadata Working Group, actively maintained, current release 4.3 from 2019-08-16 Documentation https://schema.datacite.org/ Citation For the documentation: DataCite Metadata Working Group. (2019). DataCite Metadata Schema Documentation for the Publication and Citation of Research Data. Version 4.3. DataCite e.V. https://doi.org/10.14454/7xq3-zf69 For the schema: DataCite Metadata Working Group. (2019). DataCite Metadata Schema for the Publication and Citation of Research Data. Version 4.3. DataCite e.V. https://doi.org/10.14454/f2wp-s162 Further reading Use Cases DOI creation for research data Name Digital Object Interface Protocol Focus The Digital Object Interface Protocol (DOIP) is a conceptual protocol for software applications (“clients”) to interact with “services” which could be either the digital objects or the information systems that manage those digital objects. Maintenance DONA Foundation Documentation https://www.dona.net/sites/default/files/201802/Protocol_Specification.pdf Citation Reilly S (2009) Digital Object Protocol Specification, Version: 1.0 12 November 2009 Further reading https://www.dona.net/doipv1doc https://www.dona.net/suggested-reading-documents 18 Name FAIR Digital Object Framework Focus FAIR Digital Object Framework (FDOF) is guided by the FAIR Principles and combines the powerful features from both Digital Objects and Linked Data. The FAIR Digital Object has the potential to serve as the “center of the hourglass” for an emerging Internet of FAIR Data and Services. It is giving users a definite but minimal standard to build toward, yet also the freedom to choose their own implementation paths. Maintenance Draft Standard, maintained by an international consortium Documentation https://github.com/GEDE-RDAEurope/GEDE/tree/master/FAIR%20Digital%20Objects Citation - Further reading https://www.go-fair.org/today/fair-digital-framework/ Joint Statement on FAIR Digital Object Framework Kahn R and Wilensky R (2006) A framework for distributed digital object services. International Journal on Digital Libraries 6(2): 115–123, DOI: 10.1007/s00799-005-0128-x Name FAIR Implementation Profile Focus The FAIR Implementation Profile (FIP) is a collection of FAIR implementation choices made by a community of practice for each of the FAIR Principles. Community specific FAIR Implementation Profiles are themselves captured as FAIR datasets and are made openly available to other communities for reuse. Maintenance FIP Working Group, under active development Documentation - Citation Magagna, B, et al. 2020. Reusable FAIR Implementation Profiles as Accelerators of FAIR Convergence. OSF Preprints. https://doi.org/10.31219/osf.io/2p85g Further reading https://www.go-fair.org/how-to-go-fair/fair-implementation-profile/ 19 Name Schema.org Focus Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond. Schema.org vocabulary can be used with many different encodings, including RDFa, Microdata and JSON-LD. These vocabularies cover entities, relationships between entities and actions, and can easily be extended through a well-documented extension model. These vocabularies are used by 10 mio. sites, incl. Google, Microsoft, Pinterest, Yandex and others. Maintenance W3C Schema.org Community Group Documentation https://github.com/schemaorg/schemaorg https://schema.org/docs/documents.html Citation Further reading https://schema.org/ Name Structured Descriptive Data Focus The goal of the Structured Descriptive Data (SDD) standard is to allow capture, transport, caching and archiving of descriptive data (data describing a taxon or specimen), using a platformand applicationindependent, international standard. Such a standard is crucial to enabling lossless porting of data between existing and future software platforms including identification, data-mining and analysis tools, and federated databases. Status TDWG Current (2005) standard, maintained by the TDWG Biological Descriptions Interest Group Documentation https://github.com/tdwg/sdd Citation Hagedorn G, Thiele K, Morris R, Heidorn PB 2005. Structured Descriptive Data (SDD) w3c-xml-schema, Version 1.0. Biodiversity Information Standards (TDWG) http://www.tdwg.org/standards/116 Further reading - 20 Name W3C PROV Focus Provenance is information about entities, activities, and people involved in producing a piece of data or thing, which can be used to form assessments about its quality, reliability or trustworthiness. The PROV Family of Documents defines a model, corresponding serializations and other supporting definitions to enable the inter-operable interchange of provenance information in heterogeneous environments such as the Web. This document provides an overview of this family of documents. PROV is a set of recommended standards of the World Wide Web Consortium. These include its data model, an XML schema for that model, an OWL2 ontology mapping that model to RDF, and a mapping from that ontology to Dublin Core. Maintenance W3C, maintained by the Provenance Working Group Documentation https://www.w3.org/TR/prov-overview/ Citation Further reading https://github.com/pgroth/PROVTutorial https://www.w3.org/2011/prov/wiki/Main_Page Name Web Annotation Data Model Focus The Web Annotation Data Model specification describes a structured model and format to enable annotations to be shared and reused across different hardware and software platforms. Implemented by AnnoSys (https://annosys.bgbm.fu-berlin.de/). Maintenance W3C Recommendation, The specification is an outcome from the Open Annotation Community Group and the document was published by the Web Annotation Working Group as a Recommendation, maintained by W3C. Documentation https://www.w3.org/TR/annotation-model/ Citation Further reading https://github.com/w3c/web-annotation 21 Ontologies Known relevant ontologies in a tabular format incl. information on Name, Focus, and Further reading. The ontologies are in alphabetical order. Although the list is already very comprehensive, further ontologies might be of interest or relevance during ongoing development of the DiSSCo Research Infrastructure. Name PROV-O Focus The PROV Ontology (PROV-O) expresses the PROV Data Model [PROV-DM] using the OWL2 Web Ontology Language (OWL2) [OWL2-OVERVIEW]. It provides a set of classes, properties, and restrictions that can be used to represent and interchange provenance information generated in different systems and under different contexts. It can also be specialized to create new classes and properties to model provenance information for different applications and domains. Further reading https://www.w3.org/TR/prov-o/ Name Biological Collections Ontology Focus The Biological Collections Ontology (BCO) is being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework. The goal of the BCO is to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. Further reading http://www.obofoundry.org/ontology/bco.html Name Ontology for Biomedical Investigations Focus The Ontology for Biomedical Investigations (OBI) is an integrated ontology for the description of biological and clinical investigations. It helps to communicate clearly about scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more. Further reading Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, et al. (2016) The Ontology for Biomedical Investigations. PLOS ONE 11(4): e0154556, https://doi.org/10.1371/journal.pone.0154556. http://obi-ontology.org/ https://github.com/obi-ontology/obi/wiki 22 Name Information Artifact Ontology Focus The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. It is an ontology based on a theory of document acts describing what people can do with documents. Further reading http://www.obofoundry.org/ontology/iao.html https://github.com/information-artifact-ontology/IAO Name Open Digital Specimen Ontology Focus The Ontology for open Digital Specimens (ODS) situates open Digital Specimens in the relevant OBO Foundry ontologies and extends from those roots to define the new concepts needed to support mass digitization and Digital Specimens on the Internet. Further reading https://github.com/DiSSCo/openDS/blob/master/ods-ontology/ods-ont-intro.md Name MarineTLO ontology Focus MarineTLO is a top-level ontology for the marine domain (also applicable to the terrestrial domain) to tackle the need for having integrated sets of facts about marine species, and thus to assist research about species and biodiversity. It provides a unified and coherent core model for schema mapping which enables formulating and answering queries which cannot be answered by any individual source Further reading Tzitzikas Y. et al. (2013) Integrating Heterogeneous and Distributed Information about Marine Species through a Top Level Ontology. In: Garoufallou E., Greenberg J. (eds) Metadata and Semantics Research. MTSR 2013. Communications in Computer and Information Science, vol 390. Springer, Cham. https://doi.org/10.1007/978-3-319-03437-9_29 http://www.ics.forth.gr/isl/MarineTLO/ 23 04 OUTLOOK MS Report 5.3 on “Documentation of PIDs relevant for DiSSCo technical infrastructure” due in Month 18 will further extend the list of relevant building blocks for the DiSSCo RI. Concepts to assess their technical readiness and those of other important services will be part of MS 5.2 (Implementation of concepts for sustainability of services, CMS, and overall TRL) likewise due in Month 18. The first version of the DiSSCo Knowledgebase is already running and will be demonstrated during the first DPP All Hands Meeting (Session on 19th January 2021). Feedback on the current version and further requirements will be collected. The relevant data standards, ontologies and PIDs will be available via the DiSSCo Knowledgebase, time of publication will however depend on the prioritization.