Alias;FAIRsemanticsAndSolutions;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
Export Date;03/10/2019 09.25;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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A.1 Which research communities do you support or work with?;A.1a If other, which?;A.2 What is your role or position?;A.2a If other, which?;A.3 Are you involved in an European research infrastructure (ESFRI)?;A.3a If other, which?;A.4 Which type of organization do you work in?;A.4a If other, which?;A.5 Country where your organisation is based;A.6 What is the total number of researchers (full time equivalent, FTE), including doctoral candidates, working at your institution?;B.1 What metadata standards are recommended in your community?;B.2 What is your rough estimation on the amount of researchers in your community adding bibliographic metadata (creator, title, etc) to the datasets they publish? By community, we mean the domain you specified in A.1.;B.3 What is your rough estimation on the amount of researchers in your community adding additional metadata (for ex. domain specific and provenance information) to the datasets they publish? By community, we here mean the domain you specified above.;B.4 What kind of additional metadata is normally added to the published datasets?;B.5 In your experience, are the metadata standards available well suited for your community? If not, please elaborate.;C.1 Does your community use persistent identifiers?;C.2 What kind of digital objects do you use persistent identifiers for?;C.2a If other, which?;C.3 Which identifiers are used in your community for these digital objects?;C.3a If other, which?;C.4 For what purpose are the identifiers used?;C.5 What kind of objects do you refer to in your metadata with other people’s persistent identifiers?;C.5b If other, which?;C.6 In your experience, are the identifiers available well suited for your community and the purpose you want to use them for? If not, please elaborate.;C.7 Do you also work with persistent identifiers for dynamic data objects?;C.8 Are versioning and changes in data objects clearly documented?;D.1 Does your community use semantic artefacts?;D.2 Which vocabularies and/or ontologies are recommended to be used in your community?;D.3 In your experience, are the vocabularies and/or ontologies available well suited for your community? If not, please elaborate.;D.3a Why do you think this is the case?;D.4 Which criteria do you use for selecting semantic artefacts?;D.5 How do you find and access semantic artefacts that you are using?;D.6 What type of recommendations/good practices are currently being used in your community for semantic artefacts?;D.7 Which formats are used for the semantic artefacts in your field?;D.7a If other, which?;D.8 Which licences are used for the semantic artefact in your community?;D.9 Do the semantic artefacts used in your community have defined governance policies and processes (i.e. versioning, integration of a new concept,...)? If yes or partly, please, elaborate.;D.9a Please, tell us something about the governance policies and processes;D.10 Are the semantic artefacts used in your community interoperable with each other? If partly or no, please, elaborate.;D.10a Please, elaborate.;D.11 What is the common process defined in your community to build semantic artefacts? Please, specify the type of semantic artefact if relevant.;D.12 Which tools are commonly used in your community for building semantic artefacts?;D.13 Are the semantic artefacts used in your community documented with metadata? If yes or partly, please, elaborate.;D.13a What kind of metadata?;D.14 Do you actively contribute to the development and/or maintenance of a semantic artefact used in your community? If yes, which one?;D.15 Which semantic artefacts do you contribute to?;E.1 Does your community use research software?;E.2 Is the research software that is being produced in your institute being made available to others?;E.3 Describe the process of publishing or sharing such software, including how you deal with versioning, persistent identifiers, and metadata?;E.4 What challenges do researchers in your community encounter when trying to find relevant research software on the web?;E.5 What challenges do researchers in your community encounter when trying to re-use relevant research software on the web?;Would you be willing to participate in any follow up landscape assessment activities being carried out by FAIRsFAIR?;Please give your name, email and affiliation, so that we might get in touch
;;Research infrastructure operator;;CLARIN ERIC;;Research infrastructure;;Finland;"1000<";CMDI;75 - 100%;50 - 75%;;;yes;"scientific publications;datasets;files without metadata;files containing metadata;software;metadata records;semantic artefacts (vocabularies, data models, concepts)";;URN;;;"scientific publications;datasets;files without metadata;files containing metadata;software;metadata records;semantic artefacts (vocabularies data models or, concepts);researchers";;;partly;yes;yes;Semantic vectors created by e.g. word2vec;yes;;;;;other;word2vec;CC0 or CC-BY;partly;;;;;word2vec;yes;CMDI;yes;;yes;Yes, made public;;;;no, thank you;
201-07 Bioinformatics and Theoretical Biology;;"Research support staff;Researcher;Policy maker";;;;"Research infrastructure;University";;Other country or countries;"1000<";"Bioschemas

DCC for publication data";"<10%";"<10%";;No. we need to decide on standard set of metadata schemas for genomics raw data which needs to be adopted as  standard practice. In my opinion publication data (bibliographic info is well established) but not for the raw data. ;yes;"scientific publications;datasets";;"DOI;other";SRA, EGA;;datasets;;Yes;no;no;"I don't know";;;;;;;;;;;;;;;;;;;;yes;Yes, made public;;Not well documented.;;yes, please;
204-05 Immunology;;Researcher;;;;Research institution;;Germany;500-1000;MiAIRR (Minimal Information on Adaptive Immune Receptor Repertoires);10 - 25%;"<10%";"(Data is usual DNA/RNA sequencing data):

- Type of cell from which DNA was extracted

- Species

- (some) details about experimental protocol, e.g. time point of sampling";The first release were typically not easy to use (to complicated for annotation, no ontologies, etc.), but there has been some progress over the last year or two.;yes;"scientific publications;datasets;metadata records";;DOI;;cross-referencing between data sets / metadata and data storage;"scientific publications;datasets;metadata records;researchers";;DOIs are ok to find things, but you typically end up on another HTML page. Would be better if the objects would be directly referenced.;no;partly;yes;"- NCBITAXON (for biological species names)

- CellOntology (for lymphocyte populations)

- DOID (disease classification)

- Uberon (tissue classification)";yes;;"* MUST cover the majority of the required terms, but complete coverage is OPTIONAL

* MUST have a structure that is scientifically correct and logically coherent

* MUST NOT feature complexity that makes it hard to use for queries and data representation

* SHOULD already be widely adopted

* MUST be actively maintained

* MUST be available under a free license

";Ontobee, NCBI, EBI;;"OWL;XML";;We try to use only ontologies licensed as CC-BY, but there are some topics for which only proprietary ontologies are available.;"I don't know";;partly;"- CellOntology refers to Uberon

- NCBITAXON is used by numerous ontologies that need to encode biological species";Currently we are still focusing on re-using existing artefact, not on building new ones.;not applicable;"I don't know";;no;None, but planing to (CellOntology).;yes;Yes, made public;"Publishing: Need to get clearance by Technology Transfer to license under Free Software License (e.g. GPL, Apache, MIT) first. Publishing mainly via Github (or similar Git-based source code repository), often with accompanying manuscript (i.e. ""Software Publication"").



Versioning: Via Git and higher-level feature of the repository (""Releases""). We use Zenodo for long-term availability of releases (linked via DOI).



Metadata: JSON in main directory, used by Zenodo. Mainly provides ORCIDs of the developers.";No dedicated search engine that would classify or tag software.;Mainly dependencies (i.e. software needs as special - often outdated - version of a library or another program to operate correctly / at all).;yes, please;
205-02 Public Health, Health Services Research, Social Medicine;;"Research support staff;Research infrastructure operator";;ELIXIR;;Research institution;;"Belgium;France";"1000<";"HPO Human Phenotype Ontology

ORDO Orphanet Rare Disease Ontology

HGVS Nomenclature

The FAIR Guiding Principles document for scientific data management and stewardship";50 - 75%;25 - 50%;"Diseases identifiers (OMIM, Orphanumber, ICD...)

HPO ids

HGNC ids";If used correctly, yes.;yes;"scientific publications;datasets;files containing metadata;metadata records;semantic artefacts (vocabularies, data models, concepts)";;"DOI;PURL;other";Orphanumber, HPO Ids;annotation, codification (health records), interoperability;"scientific publications;files without metadata;files containing metadata;metadata records;semantic artefacts (vocabularies data models or, concepts)";;Not always, lack of full standardisation amongst international resources;no;yes;yes;"HPO (Human Phenotype ontology)

ORDO (Orphanet rare diseases ontology)

NCIT

SNOMED

ICD

OMIM";yes;;accuracy;bioportal, fairsharing, EBI (OLS);;"OWL;RDF;XML";;various. Some CC BY, CC BY ND and other;yes;At least we know about ORDO processes managed by Orphanet (Standard operating procedures avalaible);partly;"Depends. Not always the same ""level"" of interoperability (technical or semantic)";;;;;yes;"ORDO

";yes;No;;;;no, thank you;
"205-17 Endocrinology, Diabetology;205-30 Radiology and Nuclear Medicine;206-01 Molecular Neuroscience and Neurogenetics;206-02 Cellular Neuroscience;206-04 Systemic Neuroscience, Computational Neuroscience, Behaviour;206-05 Organismic Neurobiology;206-06 Cognitive Neuroscience;206-07 Molecular and Cellular Neurology, Neuropathology;206-08 Clinical Neurosciences";;Researcher;;;;University;;Other country or countries;"1000<";In the neuroimaging community there is BIDS, NIDM and COBIDAS.  For other communities, no specific standards are recommended;75 - 100%;10 - 25%;For subject demographics and assessments - the actual definition and link to a published common data element.;In neuroimaging - the standards seem to be suited for the community and have been fairly broadly adopted.;yes;"scientific publications;datasets;software;protocols";;"DOI;PURL;other";local accession number;For identification of published artefacts;"scientific publications;datasets;software;protocols;semantic artefacts (vocabularies data models or, concepts);funders;researchers;research organisations";;;no;partly;yes;A number of ontologies and terminologies are recommended, including: FMA, UBERON, DO, GO, Chebi, NCBI Taxonomy, PATO, and a host of OBO ontologies, and some locally developed extensions;yes;;Community support and relevance to the project.;Search sites such as ontobee, ncbo bio-portal, cde portals (e.g. NLM @ NIH), interlex;;"OWL;RDF;SHACL";;;partly;Some artefacts are well governed (e.g. OBO ontologies), however, there are a number of artefacts (e.g. Common Data Elements) that don't have good governance policies.;partly;;There is no common process - depends on the artefact and the community developing them.;Protoge, RDFlib;partly;;no;;yes;Yes, made public;Software being made publicly available is made available via GItHub and uses GitHub release mechanisms;;Is the software still supported and who can one contact if there are issues;yes, please;
"206-01 Molecular Neuroscience and Neurogenetics;206-08 Clinical Neurosciences";;Research support staff;;;;"University;Medical School/Teaching Hospital";;Germany;"<100";BIDS, htf5, but mostly none;50 - 75%;"<10%";animal information;in most cases, no standard exist, and very few data is published.;no;;;;;;;;few exist, community do not know about the existing ones (MGI numbers, RRID);;;no;;;;;;;;;;;;;;;;;;;;yes;No;the existing solutions (github-zenodo) are rarely used.;;;no, thank you;
"314-01 Geology and Palaeontology;315-01 Geophysics;315-02 Geodesy, Photogrammetry, Remote Sensing, Geoinformatics, Cartography;316-01 Geochemistry, Mineralogy and Crystallography;318-01 Hydrogeology, Hydrology, Limnology, Urban Water Management, Water Chemistry, Integrated Water Resources Management";;Repository staff;;EPOS;;Research institution;;Germany;500-1000;DataCite, ISO19115, NASA GCMD DIF, FDSN;75 - 100%;50 - 75%;free keywords, contributors, funders, spatial and temporal extent;Currently a profile of ISO19115 for research data is missing to make sure information about publications is written to the same tags in the XML-tree. In addition, it is difficult to ship information about institutional identifiers and researcher identifiers. However, DataCite works quite well for this purpose.  ;yes;"scientific publications;datasets;software;semantic artefacts (vocabularies, data models, concepts);other";Samples (IGSN) - i.e. landing pages of physical samples;"DOI;URN;other";IGSN;;"scientific publications;datasets;software;funders;researchers;research organisations;other";Samples (IGSN);;yes;yes;yes;NASA Science Keywords, Platforms and Instruments, GEMET Thesaurus, GeoSciML (Geologic Time Chart, Simple Lithology);yes;;worldwide acceptance, preferably a description for each term should be found in the RDF document;listening peers and talks at confernces, there is a registry at Australian Research Data Commons;;"SKOS;RDF;XML";;;"I don't know";;"I don't know";;;Not part of such groups, but I saw Excel sheets producing RDF-XML.;yes;Not sure what metadata means - often concepts/classes contain a descriptive text;no;;yes;Yes, made public;development in public repository & assign DOIs to specific releases;a comprehensive catalog with software tagged with domain vocabulary (the software solves problems of specific research domains);;no, thank you;
"COMPUTING & RESEARCH INFRASTRUCTURES";;"Research support staff;Repository staff;Policy maker";;Other;OpenAIRE (I know that this is different project, but just want to mentioned);"Research infrastructure;University";;Other European country;"1000<";dc (Dublin Core),and OpenAIRE 3.0 compatibility;25 - 50%;10 - 25%;;All my answers are based on literature repositories as a sub-class of data repositories. Just few of our institutions started to deposit data (as an obligation from H2020).;yes;"scientific publications;metadata records;other";Authors (ORCID);"DOI;URN";;Alternative Metrics, citations;"scientific publications;metadata records;funders;researchers";;Yes they are. The researchers like all those linking which is provided by the PIDs;no;no;no;;;;;;;;;;;;;;;;;;;;no;;;;;no, thank you;
"COMPUTING & RESEARCH INFRASTRUCTURES";;Researcher;;;;University;;Austria;500-1000;;75 - 100%;75 - 100%;;;yes;"scientific publications;datasets;files without metadata;files containing metadata;software;methods;protocols;metadata records;semantic artefacts (vocabularies, data models, concepts)";;"DOI;URN";;;"scientific publications;datasets;files without metadata;files containing metadata;software;methods;protocols;metadata records;semantic artefacts (vocabularies data models or, concepts);researchers";;;partly;yes;yes;;yes;;;;;"OWL;RDF;XML";;;yes;;yes;;;;yes;;yes;;yes;Yes, made public;;;;no, thank you;
"ENERGY;104-01 General and Comparative Linguistics, Typology, Non-European Languages;201-07 Bioinformatics and Theoretical Biology";;Research support staff;;ELIXIR;;Research institution;;Belgium;"1000<";a seletion of metadata standards according to FAIRSharing web site;75 - 100%;25 - 50%;depending on the type of experiment the metadata requirements of the repositories is followed e.g. the ELIXIR Core resources;usually the metadata standards have good quality, many of the frequently used metadata standards are extended at the moment, for various areas metadata standards might have to be developed or finetuned.;yes;"scientific publications;datasets";;"DOI;PURL;other";identifiers from ELIXIR Core resources, EBI-EMBL databases and NIH data sources;retrieval of data, re-use of data, mapping of datasets to datasets from other but similar databases;"scientific publications;datasets;files containing metadata;semantic artefacts (vocabularies data models or, concepts);researchers";;mostly yes but there is a lot of room for improvement e.g. use of Orcid for researchers;"I don't know";partly;yes;e.g. EDAM ontology, for an overview https://www.ebi.ac.uk/ols/ontologies;yes;;trusting the list provided by e.g. https://www.ebi.ac.uk/ols/ontologies;see above https://www.ebi.ac.uk/ols/ontologies;use it whenever appropriate, users are encourage to use ontologies, training events about Data Stewardship etc.;OWL;;would have to look it up;yes;EMBL-EBI and ELIXIR ;partly;there are many projects in the ELIXIR Interoperability platform;I do not know the exact process ;do not know, I am an end user of semantic artefacts;yes;"e.g. Ontology IRI: 

Version IRI: 

Ontology id:

Version: 2014-12-05

Number of terms: 250

Last loaded: Fri Jul 15 21:27:33 BST 2016

date

saved-by

default-namespace

has obo format version

auto-generated-by

comment

typeref";no;;yes;Yes, made public;"publishing via groups or universities github

python tools should go to pypi

R tools should go to CRAN or BioConductor

in many cases these repositories require metadata";"there is bio.tools and other tools database, information is very disperse and not easy to find

";"issues with installation, dependencies

very good but out-dated software 

software sustainability";yes, please;
"ENERGY;ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES;PHYSICAL SCIENCES & ENGINEERING;SOCIAL SCIENCES;COMPUTING & RESEARCH INFRASTRUCTURES";;"Research support staff;Repository staff;Research infrastructure operator";;;;University;;Ireland;"<100";Domain dependent. ;"<10%";"<10%";Unsure currently;Domain dependent;yes;scientific publications;;"DOI;URN";;Requirement of publisher;scientific publications;;;"I don't know";"I don't know";"I don't know";;;;;;;;;;;;;;;;;;;;yes;No;Currently beginning to write this policy and attempting to have it adopted;Unsure currently;Unsure currently;yes, please;
"ENERGY;ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES;PHYSICAL SCIENCES & ENGINEERING;SOCIAL SCIENCES;HUMANITIES;COMPUTING & RESEARCH INFRASTRUCTURES";;Research support staff;;;;University;;Netherlands;"1000<";Dublin Core, subset of DataCite, parts of Darwin Core, KNA (Archaeology);10 - 25%;10 - 25%;method related info;More options or requirements put researchers off. Researchers in humanities & social sciences in general do not realise what types of metadata are most important and why. ;yes;"scientific publications;datasets;files without metadata;files containing metadata;software;metadata records";;"DOI;URN;Handle;other";ORCID;long term findability, reference;"scientific publications;datasets;files without metadata;files containing metadata;software;metadata records;researchers";;"Yes.

There is a lot of misunderstanding about handles vs the better marketed DOI, alas. There is no patience to learn to understand what works where and why.";partly;yes;"I don't know";;;;;;;;;;;;;;;;;;;;yes;Yes, with selected parties only;"- Within the research groups (some have a GIT-server)

- Via platforms Github, Zenodo(to lesser degree Bitbucket)

- Via DataverseNL (versioning support included)";"Finding software, 

Assessing relevancy

";"Assessing quality

Getting back to the researcher (due to short term affiliation to universities/research institutes)";yes, please;
"ENERGY;ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES;PHYSICAL SCIENCES & ENGINEERING;SOCIAL SCIENCES;HUMANITIES;COMPUTING & RESEARCH INFRASTRUCTURES";;"Research infrastructure operator;Researcher";;;;University;;Italy;"1000<";Several W3C Recommendation, as well as other ontologies used for describing bibliographic data such as RDA, BIBO, SPAR, BIBFRAME.;"<10%";"<10%";Provenance data – i.e. about who created them, what process / methodology was followed for their collection, when the data has been collected, from which sources, etc.;Yes, they are, but ofter they are not properly used.;yes;"scientific publications;datasets;files containing metadata;software;methods;protocols;metadata records;semantic artefacts (vocabularies, data models, concepts)";;"DOI;Handle;PURL";;To provide a long-term sustainable access point to the data related with the resource identified.;"scientific publications;datasets;files without metadata;files containing metadata;software;methods;protocols;metadata records;semantic artefacts (vocabularies data models or, concepts);funders;researchers;research organisations;infrastructures";;In general, yes they are. The problem, rather, is that usually they are not adopted systematically.;yes;yes;yes;SPAR Ontologies, PROV-O, DCAT, VOID.;yes;;Authoritativeness (e.g. if it is a standard or it has been made available by a trusted agent), prior knowledge on the domain, current reuse of the artefacts, examples of usage and documentation.;Description in publications, Web search engine, specialised search engines (e.g. LOV vocabularies).;Those usually derived from existing and shared development methodology.;"SKOS;OWL;RDF";;Usually, CC-BY, but also CC0 is in use.;;;partly;Theoretically speaking, yes because of the common language used for modelling the data. Practically speaking, there can be inconsistencies (logical or social) among different artefacts.;Existing and shared development methodology – e.g. NeOn, SAMOD, etc.;Ontology editors (e.g. Protege).;partly;Usually, labels and comments.;yes;SPAR Ontologies (http://www.sparontologies.net), the OpenCitations Data Model (http://opencitations.net/model).;no;;;;;;
"ENERGY;ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES;PHYSICAL SCIENCES & ENGINEERING;SOCIAL SCIENCES;HUMANITIES;COMPUTING & RESEARCH INFRASTRUCTURES";;"Research support staff;Researcher;Policy maker";;;;University;;Other country or countries;"1000<";"lots, e.g.

Dublin Core

Darwin Core

Schema.org

JATS";25 - 50%;10 - 25%;;;yes;"scientific publications;datasets;software;protocols;semantic artefacts (vocabularies, data models, concepts)";;"DOI;PURL;other";"PubMed, PMC, arXiv; database identifiers like GenBank ID or Wikidata ID";referring to the concept or resource they identify;"scientific publications;datasets;software;methods;protocols;metadata records;semantic artefacts (vocabularies data models or, concepts);funders;researchers;research organisations;infrastructures";;;yes;partly;yes;lots, e.g. https://bioportal.bioontology.org/;no;"Actually, I think they are mostly suited, but I find the binarity of these questions (here and many of the similar ones above) not very helpful.

For instance, in many areas, there are multiple overlapping vocabularies or ontologies, and some of the resulting choices are useful, others less so. Also, as research advances and research fields mature, the balance between semantics fit for specific purposes and mature semantics that can be used to build infrastructure is evolving in between the above ""yes"" and ""no"" options.";"- fitness for purpose, e.g. in terms of

  - existing workflows

  - granularity

  - community buy-in

  - licensing";"- reading

- analyzing datasets, code and workflows others have shared

- word of mouth

- conferences

- social media

- ...";;"SKOS;OWL;RDF;XML;other";ShEx;"- often no explicit license, which is a problem

- often custom-made licenses, which is a problem

- often Creative Commons licenses, which are not ideal

- sometimes CC0/ public domain";partly;Some come with regular (and often versioned) release cycles and documented changes, e.g. in terms of additions/ mergers/ splits or deprecations of concepts or with regards to identifier, timestamp or access schemes.;partly;There are frequent issues in multiple dimensions, e.g. with respect to granularity, licensing, access, multilinguality.;https://xkcd.com/927/;Whatever they key people are most comfortable with.;partly;depends;yes;"https://wikidata.org

https://jats4r.org/

";yes;Yes, with selected parties only;This varies a lot - there are cases where the entire software is open source and openly licensed and developed by a broad community but also cases where only binaries are being distributed or where sharing does not happen much within an institution or group.;"Lack of documentation, e.g. of dependencies (in terms of code and data or metadata standards, including respective versioning), licensing, example workflows, semantic annotations etc.



All of these could help make searches more fruitful.";"Lack of documentation, e.g. of dependencies (in terms of code and data or metadata standards, including respective versioning), licensing, example workflows, semantic annotations etc.



Of these, most can be worked around somewhat by skilled people, but licensing cannot, so that tends to cause frustration amongst those (rather few) who pay attention to licensing.";yes, please;
"ENERGY;ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES;PHYSICAL SCIENCES & ENGINEERING;SOCIAL SCIENCES;HUMANITIES;COMPUTING & RESEARCH INFRASTRUCTURES";;Research support staff;;;;University;;Other European country;"1000<";DataCite Metadata Schema;50 - 75%;10 - 25%;"Keywords on Methods; Geographic coordinates; Dates of data acquisition etc.; more Elaborate information is provided in README-Files; Reference to related data or publications";"Many Researchers are not inclined to provide structured metadata, in particular when no accepted community standard exists. Therefore some to many are quite happy with providing additional information in the form of README-Files instead of having to adapt to any Kind of pre-defined Schema.

Some groups collate such README-Files in a form which was at least agreed upon within their group or is at least up to the best or real practices in their field.";yes;"scientific publications;datasets;software;metadata records";;"DOI;Handle";;"DOI: Providing persistent reference to published objects; Handle (Epic): Not fully clear, probably earlier in the LifeCycle and independently from publishing";"scientific publications;datasets;software;metadata records;researchers";;DOI and ORCiD are quite suitable for the Purpose. Issues remain e.g. for the use with Software and its versioning in particular. ROR and funders-ID will be an issue sooner or later.;no;partly;"I don't know";;;;;;;;;;;;;;;;;;;;yes;Yes, made public;"A process for software disclosure and registration is in place. It allows for both Open and Closed Source Licensing. The process is managed by the Technology Transfer Office and executed in a repository which assigns DOI for the archived version of record of the code with License included. New versions can be submitted and are identified as such.

Metadata (based on DataCite Schema) is not exhaustive.";Identify current or desired version. ;Ensure Software's or Version's Integrity and understand dependencies from additional libraries etc. Be sure of the applicable License.;no, thank you;
"ENERGY;ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES;PHYSICAL SCIENCES & ENGINEERING;SOCIAL SCIENCES;HUMANITIES;COMPUTING & RESEARCH INFRASTRUCTURES";;Repository staff;;;;Private company;;"Netherlands;Other country or countries";"<100";Scholix, schema.org, Google Datasets, DataCite, Dublin Core;75 - 100%;25 - 50%;"Links to articles related to a dataset or which the datasets supplement

Links to other objects (code, other datasets)";While broad metadata standards are recognized by our partner universities they point out that community-specific ontologies will be essential for our repository to serve communities well as they are the most versed in what standards suit their specific areas the best.;yes;"datasets;files containing metadata;software;methods;protocols";;DOI;;publication, archiving,  and making data FAIR;"scientific publications;datasets;software;methods;protocols";;As a repository contributing to Scholix we embrace the DOI as the standard for the findability of links between published scholarly literature and deposited data. At the same time we recognize work that communities are making to consider other PIDs that might focus on use cases beyond publishing scholarly literature and will consider these community standards when making decisions to further develop Mendeley Data.;no;yes;yes;As we are a generic repository we are now working together with partner institutions to understand what kind of metadata/ontologies the communities they represent make use of. Based on their input we will broaden our current metadata schema (with scientific categories based on our own OmniScience taxonomy) to provide support to relevant subject area as well as institutional vocabularies.;no;The answer is more precisely: the ontology we have is suited but at at the moment only at a high level. We continue to improve our repository to meet user needs and institutional requirements on vocabularies and are incorporate custom metadata templates in our product.;see response D3a;see response D3a;Subject area/community driven semantic artifacts should be leading over institutional/organizational ones when it comes to curation of data content. For institutions metadata related to funding and organizational structure are important to demonstrate output for specific funding and to show research output and impact at institutional level.;;;;"I don't know";;"I don't know";;;;"I don't know";;no;;yes;Yes, made public;"Mendeley Data provides an open RESTful API which allows creating and editing your datasets, as well as retrieving and accessed published datasets. The API endpoints are fully documented https://api.mendeley.com/apidocs/docs#!/datasets/getLatestPublicDatasets



In addition this we have another API https://datasearch.elsevier.com/api/docs Elsevier DataSearch which powers the search in Mendeley Data and is a prototype research data search engine developed by the RDM/Mendeley Data team.";In our specific case we are working to make software more easily found via our Data Search engine by improving how we tag objects. This process of tagging is something that researchers and other stakeholders with an interest in software see as something that can generally be improved. Often discussions about research data tend to be focused on the experimental outputs and less so on the code or software that support getting to these outputs. As a result software citations are very limited and credit is not attributed.Often the software community feels therefore alienated from the discussions on standards the research data community focuses on.;The lack of citation reduces discoverability which in turn reduces chances for reuse. In  addition to this lack of metadata completeness is often also an issue for reuse in a similar way that it would be a problem for reuse of research data. ;yes, please;
"ENERGY;HEALTH & FOOD/ LIFE SCIENCES;PHYSICAL SCIENCES & ENGINEERING;COMPUTING & RESEARCH INFRASTRUCTURES";;"Researcher;Policy maker";;European XFEL;;Research infrastructure;;Germany;"1000<";Some data captured automatically at the facility, but the linkage to what the user is doing and the sample preparation information and experiment conditions is lost as this information goes into personal log books, google spreadsheets, confluence or elsewhere. ;25 - 50%;25 - 50%;Sample preparation, additional experimental conditions, beam properties, instrument configuration, photon beam configuration. ;"There are no real standards - each facility and even each beam line does it their own way. 

Critically, the linkage to what the user is doing and the sample preparation information and experiment conditions is lost as this information goes into personal log books, google spreadsheets, confluence or elsewhere. This is a huge barrier to recording the intention of the experiment, and logging what was actually done.  Without this information - currently recorded elsewhere - the data is all but encrypted. ";no;;;;;;;;"Closest identifier is experiment proposal number and data collection run within that experiment. 

This seems to be an appropriate level of generality. 

Experiment alone is too broad as often different things are done; individual files and exposures is too fine.  ";;;no;;;;;;;;;;;;;;;;;;;;yes;Yes, made public;"When done properly:  (a) A publication releasing the software; (b) a web site with information, downloads, examples, instructions and a turorial; and (c) a publicly available and maintained code repository.



Here I'm talking about well versioned software.  Unfortunately the research environment does not well reward those who do software development properly, rewarding instead those who take the shortest path to a publication and leave a software mess in their wake.  IN academia the reward is for the publication - that's what counts, not the re-usable code. ";"Quality control - knowing what works and what does not is often word of mouth, and knowing the developer personally. 

Also there is little interoperability resulting in lots of effort to re-use code from others. With limited time the barrier to re-use is high, and it's easy to be  motivated to redo it yourself. 

Things done in Jupiter are particularly hard to re-use and hard to deploy on large data sets (useful only for messing with data, not for the 'heavy lifting' of processing 700TB datasets. 



";Experiment-specific one-foo scripts written by students for a specific experiment are never archived and are not re-useable.   They exist for a specific publication at best and are not designed for re-use (as designing for re-use this takes time and effort);yes, please;
"ENERGY;HEALTH & FOOD/ LIFE SCIENCES;SOCIAL SCIENCES;COMPUTING & RESEARCH INFRASTRUCTURES;205-04 Physiology";;Repository staff;;CESSDA ERIC;;"Research infrastructure;University;Research institution";;United Kingdom;"<100";Dublin Core (for OAI-PMH), Data Documentation Initiative (DDI 2.5, 3.x etc), DataCite Metadata increasingly a de facto  requirement;50 - 75%;25 - 50%;"Coverage and methodology, time, geography, observation units. population, number of units, collection method

sampling procedures, data types, weighting, ";DDI is usually used at the study object level (DDI2.5) but DDI3.x supports a wide range of granular metadata including questions and variables. The standard is actively developed by and with the community of repositories, depositors and researchers, ;yes;"scientific publications;datasets;files containing metadata;semantic artefacts (vocabularies, data models, concepts)";;DOI;;vocabularies use identifiers, but not from a PID provider. Data sets (study level digital objects) have DOIs minted through datacite. From the client perspective the DOI refers to both the DataCite metadata and the object (resolves to a jump page with an object history). ORCIDS for researchers. ;"scientific publications;datasets;files without metadata;files containing metadata;software;metadata records;semantic artefacts (vocabularies data models or, concepts);funders;researchers";;Organisational PIDs are still not fully mature. PIDS for methods and protocols have their own challenges and like some other areas (semantic artefacts) would benefit from being referenceable and managed in trusted, FAIR metadata registries. ;partly;partly;yes;"We have some internal CVs (or at least controlled lists) but participate in the creation and management of DDI controlled vocabularies. 

We also use the European Language Social Science Thesaurus (ELSST) which is a broad-based, multilingual thesaurus for the social sciences.

These are/will be part of the CESSDA technical framework and CESSDA will also support other users of DDI by providing access to DDI CVs";yes;;"Community approval/demand

Quality (completeness, etc)

Ease of use (formats, supporting technology etc)

Well managed (curated, versioned etc)

";Primarily through the community (and our contributions to that community). But centralised registries of these semantic artefacts (trusted and FAIR) would be ideal);Standardised not ad hoc. in a standard format. Formally managed and versioned with changed communicated. ;"SKOS;OWL;RDF;XML";;Metadata are, by default, made freely available for use and reuse unless explicitly precluded by third party rights or licences. ELSST is subject to a licence. ;partly;There are committees and there are rules and there are version policies. But these don't all take account of the structure (semantic) vs content (best practice) vs consuming application (do I need to update my tool based on the change to your semantic artefact?);partly;Semantically you can play with ELSST or any other SKOS vocabulary in KOSMOS. But that doesn't mean the content is 'interoperable'. Two projects using DDI might use different profiles and therefore only be partially interoperable. This  ;Identify a need, consult, test, iterate, deploy, manage. ;Historically in rectangular data or other text-based formats. Increasingly in standard tools like Skosmos. ;partly;identifiers, descriptions, licences, ;yes;DDI, ELSST;yes;Yes, with selected parties only;Practices are extremely variable with non-commercial tools which don't apply semantic best practices.  There's a real need for agreed minimal practice in development and deployment, ;We need trusted FAIR registries of software with rich metadata which are managed over time (remain accurate and sustainable);Research projects are rife with 'pre-release' software which isn't ready for operation, let alone documented and managed. There's a real need for agreed minimal practice in development and deployment, ;;
ENVIRONMENT;;"Research support staff;Repository staff";;"DiSSCo;Other";Not specifically ESFRI, but involved in many oceanographic and polar data infrastructures. Examples: SeaDataNet/SeaDataCloud, EMODnet, IODE ODP, SCADM, ADC, SOOS, etc.;Research institution;;Netherlands;100-500;"- Common Data Index (CDI) of SeaDataNet (www.seadatanet.org)

- Directory Interchange Format (DIF) of CEOS/IDN (and NASA's Global Change Master Directory (GCMD) for polar data

- Darwin Core for biological data

- OBIS/ENV for oceanographic biological and environmental data

- Schema.org";"<10%";75 - 100%;"We have a problem with questions B2 and B3:

Both in oceanographic as well as in polar research data, the metadata are generated by the data center or data repository. So the amount of researchers adding bibliographic or domain specific metadata would be zero, whereas all data would have full domain specific metadata.";All standards were specifically developed by and for these communities;yes;"scientific publications;datasets;protocols;metadata records;semantic artefacts (vocabularies, data models, concepts)";;"DOI;URN;Handle;other";Common Data Index (CDI), UUID, DIF-ID;Identify (meta)data records;"scientific publications;datasets;protocols;metadata records;semantic artefacts (vocabularies data models or, concepts);researchers;research organisations";;Yes, see also B5;no;partly;yes;"NERC Vocabularies

GCMD keywords

WoRMS

";yes;;Semantic artefacts are usually selected by the projects or communities we participate in.;"Semantic artefacts are usually selected by the projects or communities we participate in.

All projects provide interfaces to these artefacts";See D2;"SKOS;OWL;RDF;XML";;CC-by and CC0;yes;"The NERC vocabularies are being governed by the global Seavox community with the British Oceanographic Data Centre (BODC) as lead.

The GCMD Keywords are being governed by the global CEOS/IDN community with the Global Change Master Directory (GCMD) as lead.

Similar for the World Register of Marine Species (WoRMS)

";yes;;For the NERC Vocabularies: The Vocab Builder;For the NERC Vocabularies: The Vocab Builder;yes;Name of contributor, date of contribution/change;no;None;yes;;"We don't produce research software in our institute.

We answered question E1 for our community and then got a question about our institute (?)";Don't know;Different operating systems;yes, please;
ENVIRONMENT;;Other;software development manager;eLTER;;Research institution;;United Kingdom;100-500;Gemni 2.3;75 - 100%;75 - 100%;Contextual metadata such as data generation methods and protocols, transformation steps (ETL), values and units, technical calibration of instruments if applicable, quality control and validation.;Generally yes as most environmental data generated have a spatial relevance i.e. they can be related to somewhere on earth. However the metadata standard is not so well suited to the some data from the microbiological community.;yes;datasets;;DOI;;Data publication;"scientific publications;datasets;software;metadata records;semantic artefacts (vocabularies data models or, concepts);funders;researchers;research organisations";;;no;yes;yes;"GEMET Vocab

CHEBI

EnvTHES

GCMD

Prov ontology";yes;;Ease of access and use;Through the community;We follow guidance under the NERC Vocabulary service;"SKOS;OWL;RDF;XML";;Unknown;yes;If they are managed by the NERC Vocabulary Service they fall under full strict governance https://www.bodc.ac.uk/resources/vocabularies/vocabulary_editor/ ;yes;;Mainly through discussions with domain experts in the community;We use Top Braid enterprise;"I don't know";;"I don't know";;yes;Yes, made public;We mainly publish in GitHub under a GNU General public licence;Is it discoverable and well described.  The use of GitHub and markdown has improved this but a lot of research software is still held within institutes which makes it difficult to find;Is it well documented, is it supported, upto date and and relevant;no, thank you;
ENVIRONMENT;;Repository staff;;eLTER;;Government/local government;;Austria;100-500; ISO 19115/19139, EML, INSPIRE EF;"<10%";"<10%";Parameters, site information, keywords;yes;yes;"datasets;semantic artefacts (vocabularies, data models, concepts)";;Handle;;to be able to reference across digital objects;"scientific publications;datasets";;yes;no;partly;yes;EnvThes, ENVO, NERC Vocabularies;yes;;community agreed terminology;through DEIMS and semantic repositories like AgroPortal, EcoPortal;Recommendations are under development;"SKOS;OWL;XML";;don't know;partly;EnvThes and ENVO use github issues, but for EnvThes this is not yet standard, as people still approach  the coordinator via email;partly;we need to work on harmonising variables (observable properties);EnvThes has an editorial group with domain experts from the eLTER community which decides how to implement requests from the wider community.;TopBraid;yes;source of definitions, date of change, author;yes;EnvThes;no;;;;;no, thank you;
ENVIRONMENT;;"Research infrastructure operator;Researcher";;EURO-ARGO ERIC;;"Research infrastructure;University;Research institution";;Germany;500-1000;ISO 19115, Dublin Core, Darwin Core, DIF, Schema.org, Datacite Metadata Schema;75 - 100%;25 - 50%;All metadata elements required for data citation, e.g. title, author, year, published, doi. in addition, metadata such as project & funder, instrument, abstract, license.;The suitability of the metadata standards depend on the applications within a community. different application may require different level/coverage of metadata. in the case of data citation and search purposes, the current standards are sufficient.;yes;datasets;;DOI;;data publicaition;"scientific publications;datasets;semantic artefacts (vocabularies data models or, concepts);funders;researchers;research organisations;infrastructures";;Yes for datasets (persistent identifiers for ontological terms are still missing, and also consider taxonomies and glossaries);"I don't know";yes;yes;taxonomies (itis, worms), ontologies (e.g., qudt, pato,envo), gcmd...;"I don't know";;ease of access and documentation, coverage, and sustainability of artifacts;google to find terminology portals..and use the supported API (e.g., REST).;;SKOS;;Not sure;yes;versioning are indicated by update date in metadata/;"I don't know";;we are users of semantic artifacts,no providers..;not applicable;yes;this question is unclear..;no;;no;;;;;no, thank you;
ENVIRONMENT;;Researcher;;"EU-SOLARIS;Other";SeaDataNet;Government/local government;;United Kingdom;"<100";ISO 19115, Dublin Core Metadata, SKOS ontology, DCAT, PROV, OGC standars (sensorML, O&M);25 - 50%;25 - 50%;geospatial, format, observable property, instrument, cruise etc;Yes, they are sufficient.;;;;;;;;;;;;yes;NVS, CheBI, PROV, SKOS, DCAT, DBpedia, schema.org;yes;;"-Be used by others

-Amount of users

-Coverage

-Support

-Speed

-Governance

-Activity

";Search and ask my community;;"SKOS;OWL;RDF;XML";;Creative Commons;yes;;partly;Most vocabularies use SKOS and RDF and ontologies use OWL;I don't understand the question.;Protege, ad hoc ones;yes;;yes;NVS;;;;;;;
ENVIRONMENT;;"Research infrastructure operator;Researcher";;LifeWatch ERIC;;"Research infrastructure;Research institution";;Italy;100-500;"Ecological Metadata Language

ISO 19115/19139

Darwin Core

";10 - 25%;"<10%";Provenance information;Yes but it is not exist a unique community standard.;no;;;;;;;;;;;yes;"LifeWatch Thesauri

EnvThes

Top Thesaurus

Agrovoc

Anaee Thesaurus

OBOE

ENVO

LifeWatch Core Ontology

CIDOC-CRM 

BODC Vocabularies

Research Vocabularies Australia

Observations & Measurements";no;The existing vocabularies/ontologies not cover all concepts of the domain and there is not harmonization among terminological resources.;We select semantic artefacts with definition for the concepts and standard formats.;Through web repository of semantic resources as OBO, BioPortal, AgroPortal, EcoPortal etc..;"LifeWatch Italy Thesauri Documentation (http://www.lifewatchitaly.eu/web/lifewatch-italia/reports)

W3C Recommentadions

";"SKOS;OWL;RDF;XML";;Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International ;yes;LifeWatch Italy Thesauri Documentation (http://www.lifewatchitaly.eu/web/lifewatch-italia/reports);yes;;LifeWatch Italy Thesauri Documentation (http://www.lifewatchitaly.eu/web/lifewatch-italia/reports);TemaTres, VocBench and Protegé.;partly;Title, creator, contributor, publisher, rights, subject, description, date, modified, language;yes;LifeWatch Italy Thesauri and LifeWatch Core Ontology;yes;No;;;;yes, please;
ENVIRONMENT;;"Research infrastructure operator;Researcher";;IAGOS;;"Research infrastructure;Research institution";;Germany;100-500;Cluster metadata standards are currently developed in the framework of the ESFRI cluster project ENVRI-FAIR. There are subdomain-metadata standards applied but no standards for the  entire cluster yet agreed.;10 - 25%;"<10%";Responsible researcher, instrument-specific information.;;yes;"scientific publications;datasets";;DOI;;for publication purposes;"scientific publications;datasets";;;"I don't know";partly;"I don't know";The development of vocabularies and ontologies is ongoing part of the project work.;;;;;;;;;;;;;;;;;;;yes;Yes, with selected parties only;Software is developed and published via GITlab and similar tools.;;;yes, please;
ENVIRONMENT;;"Research support staff;Repository staff";;IAGOS;;"Research infrastructure;Research institution";;France;"<100";ISO 19115 / INSPIRE;75 - 100%;25 - 50%;provenance, data policy/data licence, extent, acknowledgement;yes;yes;"scientific publications;datasets;software;metadata records";;DOI;;citation, provenance;"scientific publications;datasets;software;researchers;research organisations;infrastructures";;yes;yes;partly;no;GCMD, NetCDF CF;;;;;;;;;;;;;;;;;;;no;;;;;no, thank you;
"ENVIRONMENT;201-07 Bioinformatics and Theoretical Biology";;Researcher;;;;"University;Research institution";;Germany;100-500;for example MIMARKS, MIxS;10 - 25%;10 - 25%;provenance, geographical coordinates;yes;yes;"scientific publications;datasets;software";;"DOI;other";pid;re-usability, findability;"scientific publications;datasets;software";;yes;"I don't know";partly;yes;EnvO;yes;;domain specification;http://www.environmentontology.org/Browse-EnvO;unknown because not being discussed;"OWL;RDF;XML";;unknown;"I don't know";;yes;;unknown;Protege for ontologies;yes;definitions, terms and external IDs (wikidata);yes;building an own ontology and integrating it into existing ones;no;;;;;no, thank you;
"ENVIRONMENT;202-01 Evolution and Systematics of Plants and Fungi;202-02 Plant Ecology and Ecosystem Analysis;409-04 Operating, Communication, Database and Distributed Systems;409-06 Information Systems, Process and Knowledge Management";;Researcher;;DiSSCo;;Research institution;;Belgium;"<100";"Ecological Metadata Language (EML)

Darwin Core";25 - 50%;25 - 50%;identifiers for specimens;"In general yes, but there are areas were that standards are weak.

Also, the standards are so loose and poorly defined they are not as useful for data intergration as one would like.

More controlled vocabularies for important fields would really help.";yes;"scientific publications;datasets;files without metadata;files containing metadata;semantic artefacts (vocabularies, data models, concepts);other";specimens, taxonomic names;"DOI;URN;PURL";;to cite resources and to link datasets together;"scientific publications;datasets;semantic artefacts (vocabularies data models or, concepts);researchers";;They are OK, but they are not as widely adopted in the community as we would like.;yes;"I don't know";yes;"Darwin Core and its extensions

ABCD and its extension

ISO 3166

World Geographical Scheme for Recording Plant Distributions (WGSRPD)

Taxonomic names from International Plant Names Index ";yes;;"compatability with software

acceptance by the community

recommendation of standards organizations

scientific needs

";Google and the internet;;"SKOS;OWL;RDF;XML";;"CC0

CC-By";yes;Most of our standards are governed bt the Biodiversity Information Standards (TDWG) organization;partly;mapping between standards have been made and there is generally effort to be interoperable. ;"I find it a bit caotic. It is mainly based on one or a few people making the effort to push standards through, because they have a need for them or they really feel it is worthwhile.

It is generally time consuming, there is little credit and no obvious route to success.";;partly;mostly text;yes;Darwin Core;yes;Yes, made public;This is only done sometimes, but we generally use GitHub or Zenodo;"a lack of back compatibility

loose standards

cryptic documentation";as above;yes, please;
"ENVIRONMENT;202-02 Plant Ecology and Ecosystem Analysis;202-04 Plant Physiology;203-03 Animal Ecology, Biodiversity and Ecosystem Research;207-02 Plant Cultivation and Agricultural Technology;207-04 Ecology of Agricultural Landscapes;313-02 Oceanography;409-04 Operating, Communication, Database and Distributed Systems;409-06 Information Systems, Process and Knowledge Management;Other";Marine ecology, semantic web, data standards;Research support staff;;"AnaEE;EMPHASIS;Other";Go FAIR IN;Research institution;;France;"1000<";Dublin core and all W3C recommandations;25 - 50%;"<10%";"Dublin core component is the core ontology

actually, we ve just implemented PROV-O recommandations";Not always, because it is time consuming and sometime, the heterogeneity of data make it really difficult. For exemple, traceability of each transformation from image to text data need to use 4 or 5 independant processes;yes;"scientific publications;datasets;files without metadata;methods;protocols;metadata records;semantic artefacts (vocabularies, data models, concepts);other";ar each data;"DOI;Handle;other";URI, and in the future URI with ePIC recommendation format;each phenotyping object and each measurement;"scientific publications;datasets;files without metadata;methods;protocols;metadata records;semantic artefacts (vocabularies data models or, concepts);researchers;infrastructures;other";each data value, as far as possible;Not always. For exemple, national institutes cas change their name (e.g. inra and IRSTEA became INRAE). And DOI can't identify each value associated at a given time at an object.. URI are not standardised for complex systems of variables;partly;partly;yes;all linked data vocabularies, but implementation is partial and depending on the means of each stakeholders;no;only partially;"ouch... not easy to summarize.

Please free to reuse this poster focussing on our recommandations for indexing and naming variables :

David Romain, Hollebecq Jean-Eudes, Cabrera-Bosquet Llorenç, Ćwiek-Kupczyńska Hanna, François Tardieu, & Pascal Neveu. (2019). Identifying, naming and interoperating data in a Phenotyping platform network : the good, the bad and the ugly. (Version V1.0). Zenodo. http://doi.org/10.5281/zenodo.3402948

";it depends of the specialisation.W3C and agroportal are good references to access semantic artefacts;"again, please see it in

David Romain, Hollebecq Jean-Eudes, Cabrera-Bosquet Llorenç, Ćwiek-Kupczyńska Hanna, François Tardieu, & Pascal Neveu. (2019). Identifying, naming and interoperating data in a Phenotyping platform network : the good, the bad and the ugly. (Version V1.0). Zenodo. http://doi.org/10.5281/zenodo.3402948";"SKOS;OWL;RDF;XML;other";Publication in progress about that;mostly CC-BY-NC-SA , CC-BY-NC, or CC-BY depending on the grant and data governance;partly;All new implementations are community approved;partly;job in progress. Perfect interoperability is a graal but dont exist in distributed information systems because data evolve quicker than standards;"Before building, looking for what exist and enrich it.

see details at: 

David Romain, Hollebecq Jean-Eudes, Cabrera-Bosquet Llorenç, Ćwiek-Kupczyńska Hanna, François Tardieu, & Pascal Neveu. (2019). Identifying, naming and interoperating data in a Phenotyping platform network : the good, the bad and the ugly. (Version V1.0). Zenodo. http://doi.org/10.5281/zenodo.3402948";Protege ;yes;community approved vocabularies, and ontologies from linked data;yes;in progress, plant phenotyping vocabularies (MIAPPE, crop ontology...);yes;Yes, made public;"Git hub repository

see 

Neveu, P. , Tireau, A. , Hilgert, N. , Nègre, V. , Mineau‐Cesari, J. , Brichet, N. , Chapuis, R. , Sanchez, I. , Pommier, C. , Charnomordic, B. , Tardieu, F. and Cabrera‐Bosquet, L. (2019), Dealing with multi‐source and multi‐scale information in plant phenomics: the ontology‐driven Phenotyping Hybrid Information System. New Phytol, 221: 588-601. doi:10.1111/nph.15385";"a lot!

some examples :

software management plan

software versionning is a key challenge for provenance

retrocompatibility of new versions...";well understanding the future effort for accurancy and reproductibility;yes, please;
"ENVIRONMENT;202-02 Plant Ecology and Ecosystem Analysis;203-03 Animal Ecology, Biodiversity and Ecosystem Research;204-02 Microbial Ecology and Applied Microbiology;207-01 Soil Sciences;207-04 Ecology of Agricultural Landscapes;207-08 Forestry;313-01 Atmospheric Science;313-02 Oceanography;315-02 Geodesy, Photogrammetry, Remote Sensing, Geoinformatics, Cartography;317-01 Physical Geography;318-01 Hydrogeology, Hydrology, Limnology, Urban Water Management, Water Chemistry, Integrated Water Resources Management";;Other;data manager;;;University;;Other country or countries;;Ecological Metadata Language;10 - 25%;"<10%";descriptions of the data tables (or other data objects), and measurements therein;yes;yes;"scientific publications;datasets;files containing metadata;metadata records;semantic artefacts (vocabularies, data models, concepts)";;"DOI;PURL";;persistence, reliability ;"scientific publications;datasets;metadata records;semantic artefacts (vocabularies data models or, concepts);researchers;research organisations";;somewhat. Personally, I am not aware of PIDs for software, methods. The PIDs for funders and organizations are either nascent or underused. ;no;yes;yes;BCO, ENVO, CHEBI, PATO, OCL, UO, OBI, OBOE;yes;;"1. coverage of the domain

2. completeness

3. expressed in W3C-recommended languages (OWL, RDF)

4. adherence to Open Biomedical Ontologies (OBO) practices 

5. maintenance model which ensures IDs are indeed permanent";OBO, personal research, word-of-mouth;See D.4;"SKOS;OWL;RDF";;general CC-0, CC-BY;partly;These tend to be unpublished. for the most part, we rely on trust;partly;some terms, to some extent;One could write a whole paper on this.;Protege ;partly;RDF annotation properties;yes;ENVO, OBOE;;;;;;;
"ENVIRONMENT;COMPUTING & RESEARCH INFRASTRUCTURES";;Research infrastructure operator;;;;Research infrastructure;;Germany;"1000<";"DataCite

Climate Forecast Conventions (CF Conventions)

Earth System documentation (es-doc)";25 - 50%;"<10%";"Scientific variables, units and dimensions

Geospatial coordinates and grids";The standards used for data citation, referencing and describing interoperability, findability, and provenance lack precision to describe the data at multiple levels of granularity, which is neccessary to cover scenarios beyond simple citation. Data cannot be made fully FAIR with the existing standards.;yes;"scientific publications;datasets;files containing metadata";;"DOI;Handle";;providing citable references, providing identification before formal publication (initial data sharing);"datasets;files containing metadata;metadata records";;"The identifiers and their management processes and infrastructures are not scalable to the large number of objects they should be assigned to.

In addition, the metadata associated with them lacks detail to make data fully FAIR across the whole scientific workflow before publication.";no;partly;no;Ontology usage has been tried in the past but never reached more than prototypic stage due to challenges involved in capturing the information adequately from researchers.;;;;;;;;;;;;;;;;;;;yes;Yes, with selected parties only;Some software (data tools, service components) is openly shared via github, zenodo or similar open repositories. There is no coherent approach to describing them with metadata beyond the mechanisms these individual repositories offer.;;;yes, please;
"ENVIRONMENT;COMPUTING & RESEARCH INFRASTRUCTURES;101-01 Prehistory;201-03 Cell Biology;201-06 Developmental Biology;201-07 Bioinformatics and Theoretical Biology;201-08 Anatomy;202-01 Evolution and Systematics of Plants and Fungi;202-02 Plant Ecology and Ecosystem Analysis;202-04 Plant Physiology;202-05 Plant Biochemistry and Biophysics;202-06 Plant Cell and Developmental Biology;202-07 Plant Genetics 203-01 Special Zoology and Morphology;203-02 Evolution, Anthropology;203-03 Animal Ecology, Biodiversity and Ecosystem Research;203-04 Sensory and Behavioural Biology;203-05 Animal Physiology and Biochemistry;203-06 Evolutionary Cell and Developmental Biology (Zoology);204-01 Metabolism, Biochemistry and Genetics of Microorganisms;204-02 Microbial Ecology and Applied Microbiology;204-03 Medical Microbiology, Parasitology, Medical Mycology and Hygiene, Molecular Infection Biology;204-04 Virology;205-05 Nutritional Sciences;207-01 Soil Sciences;207-03 Plant Nutrition;207-05 Plant Breeding;207-08 Forestry;305-01 Biological and Biomimetic Chemistry;313-01 Atmospheric Science;313-02 Oceanography;314-01 Geology and Palaeontology;315-01 Geophysics;315-02 Geodesy, Photogrammetry, Remote Sensing, Geoinformatics, Cartography;316-01 Geochemistry, Mineralogy and Crystallography;317-01 Physical Geography;406-05 Biomaterials";;Other;technical coordinator;DiSSCo;;"Research infrastructure;Other";Natural History Museum;Netherlands;100-500;TDWG standards, e.g. DarwinCore, ABCD, ABCDEFG;75 - 100%;75 - 100%;what, where, when, by whom, persistant identifiers;yes, but not without problems, some concepts are ambiguous, missing standard vocabulaires, difficult to improve standards (depends on volunteers);yes;"scientific publications;datasets;metadata records;other";specimen, samples;"DOI;URN;Handle;ARK;PURL;other";CETAF Identifiers, see https://cetaf.org/cetaf-stable-identifiers;persistant identification, resolving data, linking data, provenance;"scientific publications;datasets;funders;researchers;research organisations";;too many different systems and each institute has their own protocol for using identifiers;yes;no;no;;;;;;;;;;;;;;;;;;;;yes;Yes, made public;published on github, no rules for versioning, identifiers or metadata;not always easy to find by google, difficult to estimate the quality and fitness for purpose.;quality is usually low, works only for a specific purpose, not maintained, poorly documented, buggy;yes, please;
"ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES";;Researcher;;EMBRC ERIC;;Research institution;;Italy;100-500;don't know;25 - 50%;10 - 25%;don't know;no, don't know;"I don't know";;;;;;;;don't know;;;"I don't know";don't know;;;;;;;;;;;;;;;;;;;no;;;;;yes, please;
"ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES";;Researcher;;;;University;;France;"1000<";DCAT, OMV, Schéma.org, DCT, Prov-O, plus all’the standard sem web languages ;50 - 75%;25 - 50%;See the paper : https://link.springer.com/article/10.1007/s13740-018-0091-5;"See the paper 

https://hal-lirmm.ccsd.cnrs.fr/lirmm-01605783/document";yes;"files without metadata;semantic artefacts (vocabularies, data models, concepts)";;"DOI;PURL;other";URI ;They are the basis of the semantic web;"scientific publications;datasets;semantic artefacts (vocabularies data models or, concepts);other";License, language, formats;Yes. See our paper where this is is discussed. ;no;partly;yes;See BioPortal, AgroPortal ;yes;;See our paper on the NCBO Recommender;Via ontology repositories;Multiples including OBO principles and follow Sem Web standards. ;"SKOS;OWL;RDF";;Open;partly;Depends of the maturity of the projects;partly;See paper on mappings in BioPortal;"Neon methodology 

OBO principles

Ontology 101

Etc";"Protege

ThesauForm 

VocBench

Addoc ";yes;MOD 1.2;yes;Multiple in the agro/bio domains. Only technical contributions not content. ;yes;Yes, made public;No exists ;Hard;"Installation

Complexity

Documentation

Multiple choices

Discover ";yes, please;
"ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES;207-07 Agricultural Economics and Sociology;407-06 Biomedical Systems Technology";;"Research support staff;Repository staff";;"AnaEE;EMPHASIS;ELIXIR";;Research institution;;France;"1000<";"Dublin Core for general metadata elements

Domain communities can have their own metadata standards for more specific elements, e.g. the Metadata vocabulary for Ontology Description (10.1007/978-3-319-70863-8_17) derived from OMV and implemented in the institutional repository

Some researchers from INRA use the INSPIRE, ISA-TAB... which are not implemented in the institutional data repository.

Indeed very difficult to tell as the scope of Inra is very large and many researchers publish data in a variety of domain or generic repositories. 

In the following, I provide estimations for the institutional repository Data Inra only ";25 - 50%;"<10%";As for semantic resource in our institutional repository, producers indicate what the resource was designed for and its known usages. They also provide information on the format and serialization type, e.g. owl/xml;"In the community of agriculture and nutrition, very few standards adapted to the scientific domains are available to provide rich metadata. There are some exceptions with e.g. the community of genomics

More information can be found in section 4.2 of the RDA Agrisemantics  WG report called ""Landscaping the Use of Semantics to Enhance the Interoperability of Agricultural​​Data""  you can find here : https://www.rd-alliance.org/system/files/documents/Deliverable1%20-%20Landscaping.pdf ";yes;"datasets;files without metadata;files containing metadata;semantic artefacts (vocabularies, data models, concepts)";;"DOI;URN";;access and citation mainly;"scientific publications;datasets;semantic artefacts (vocabularies data models or, concepts)";;As far as I know, yes;yes;partly;yes;"Many!

A great number of the publically available semantic artefacts is accessible from the AgroPortal http://agroportal.lirmm.fr/ dedicated to agriculture and food. Others can be found on BioPortal (https://bioportal.bioontology.org/) and EBI Ontology lookup (https://www.ebi.ac.uk/ols/index) both dedicated to biomedical domains (in the scope of Inra but not sufficient). The Agrisemantics Map of Standards provides a catalog of both accessible and non accessible (in the FAIR point of view) semantic resources of interest to our community . See its analysis in the Agrisemantics Landscaping report cited above";no;"Some domains are well equiped with semantic resources and may even suffer from proliferation while others are totally lacking of them. This point is also developed in the Landscaping report. See also the analysis of community requirements made by the RDA Agrisemantics WG: https://www.rd-alliance.org/deliverable-2-use-cases-and-requirements 

The GO FAIR Food Systems Implementation Network (https://www.go-fair.org/implementation-networks/overview/food-systems/) as well as the French ANR projects D2KAB (http://d2kab.strikingly.com/) and FooSIN will contribute to facilitate the use and creation of FAIR semantic artefacts to handle FAIR data.";"Most of the time, people tend to select the most popular but there is at this time no easy way to assess if these popular semantic artefacts are actually used.

Agroportal offers services to help identifying the most suited ontology or thesauri for your topic (based on text annotation) and metadata elements on usage and purpose. 

The D2KAB project aims to develop usage metrics to help choosing a semantic resource in Agroportal";"I use Google to find and locate them

Generally, I get them on domain portals like Agroportal. Sometimes I contact the producers (I did this morning) and they send it to me.";"We try to publish semantic resources as much as possible in standard formats, using open licenses and describe them with rich metadata, thus following the FAIR principles.

To complete my answer, I invite you to read the 3d and final output of the Agrisemantics WG, namely its recommendations : ""39 Hints to Facilitate the Use of Semantics for Data on Agriculture and Nutrition"" that wan be found on the RDA website https://www.rd-alliance.org/group/agrisemantics-wg/outcomes/39-hints-facilitate-use-semantics-data-agriculture-and-nutrition 

We are actually looking for adopters of the recommendations that are targeted to not only our community of data producers and managers but also application developers, semantic experts and funders. Our recommendations go beyond the agri-food community and could benefit to many others.

The Agrisemantics WG would be grateful if the FAIRsFAIR project could help in reaching the relevant actors!  ";"SKOS;OWL;RDF;XML;other";OBO;mainly CC-BY;partly;"Some major resources like Agrovoc have an editorial commity and rules of participation, same for ATOL, AHOL and EOL at Inra

Others use collaborative tools like gits to handle versioning and collaborative aspects

There are many different ways to do but many resources are not ""governed"" and are even not maintained";partly;"For those published in SKOS, I'd say yes

For those in OWL I'd say partly or sometimes just syntactically interoperable

But MANY resource still remain in Excel sheets!



If we consider semantic interoperability, it is a difficult issue as we have many different points of views (granularity, sharpness, domain specialty...) from one artefact to another even if some concepts are shared. 

The GACS project built a large set of alignments between 3 major semantic artifacts of the domain, namely Agrovoc, NAL thesaurus and CAB thesaurus. A foreseen follow up of this work is to use this set as a hub of concepts to align many semantic artefacts (ontologies and thesauri) and thus create bridges between them.

See https://agrisemantics.org/GACS/   ";"There is no common process at this time and no shared methodology.

The recommendations of Agrisemantics advocate for reusing existing resources, align them to each others, build and publish small, modular, reusable artefacts.  

We mostly use and produce ontologies and thesauri with an unclear frontier bewteen both (we have highly lexicalized artefacts called ontologies that look more like thesauri)";"The Agrisemantics landscaping report again will provide valuable information on this point. The most used  to edit, align and publish are listed.

But these tools are NOT adapted to our community ! They are not user friendly, show jargon terms from semantic specialists, are not graphical enough, not collaborative enough, to hard to install... only the bravest do use them. We could have much more semantic artefact producers and RE-USERS if some progress was made. We have listed a set of wanted advances in the Agrisemantics recommendations. Please read and share with people who are able to help us!  ";partly;ODM (from OMV) in Agroportal, Dublin Core;yes;"I contribute to some resources of the LovInra slice of Agroportal, especially on the metadata, licenses, URis, ... i.e. findability and accessibility

I publish some of them in our institutional triple store ";yes;No;"I don't understand what you mean by ""research software"", e.g. ""R"" ?  I will not answer this part of the survey as I feel I am not the appropriate person";I will not answer this part of the survey;I will not answer this part of the survey;yes, please;
"ENVIRONMENT;HEALTH & FOOD/ LIFE SCIENCES;PHYSICAL SCIENCES & ENGINEERING;SOCIAL SCIENCES;HUMANITIES";;"Research support staff;Repository staff;Research infrastructure operator";;Other;Institutional;"Research infrastructure;Research institution";;France;"1000<";All, if appropriate for a domain/discipline like DDI, GIS, EML, … and general Standards (Futur Use) like DCAT, PAV, FOAF, DC, DCTERMS, PROV-O, ISA-TAB...;"<10%";10 - 25%;scientific metadata;More or less, but researchers often have specific scientific metadatas, relating to their research or even dataset;yes;"scientific publications;datasets;files containing metadata;metadata records";;"DOI;Handle;ARK";;retrieval;"scientific publications;datasets;metadata records;researchers";;yes but other Object/Resource nead Persistents Identifiers : Project, Funding, Affiliation, ...;yes;no;yes;i Don't know;"I don't know";;identifier or labels;web Tools, local files, ...;if possible choose the best known standards ;"SKOS;OWL;RDF;XML";;Open;no;;partly;depending of e-infrastructure for human reading;collaboration between researcher, data librarians and Infrastructure designers;Protégé, XML editors, proprietary tools for terminology;no;;yes;FAIR schémas, Thesaurii;yes;;Software Heritage, SMP;avability for his/her research;avability for his/her research, Open or Not, license;yes, please;
"ENVIRONMENT;PHYSICAL SCIENCES & ENGINEERING;COMPUTING & RESEARCH INFRASTRUCTURES";;Researcher;;;;University;;Germany;"1000<";own;10 - 25%;10 - 25%;;;yes;"scientific publications;datasets;software";;DOI;;citations;"scientific publications;datasets;software";;;no;partly;yes;;"I don't know";;usage by others;;;"OWL;RDF";;;partly;;partly;;;;partly;;no;;yes;Yes, made public;;missing licenses;missing licenses, old software: needs adaptation to modern environments;no, thank you;
"ENVIRONMENT;PHYSICAL SCIENCES & ENGINEERING;COMPUTING & RESEARCH INFRASTRUCTURES;201-01 Biochemistry;201-06 Developmental Biology;301-02 Organic Molecular Chemistry;302-03 Theory and Modelling;303-01 Physical Chemistry of Molecules, Interfaces and Liquids - Spectroscopy, Kinetics;304-01 Analytical Chemistry, Method Development (Chemistry);313-02 Oceanography;409-02 Software Engineering and Programming Languages;409-05 Interactive and Intelligent Systems, Image and Language Processing, Computer Graphics and Visualisation;409-06 Information Systems, Process and Knowledge Management";;Repository staff;;EURO-ARGO ERIC;;Research infrastructure;;Spain;"<100";"CF Conventions

NERC vocabularies

SeaDataNet system

DataCite schema";75 - 100%;25 - 50%;"Time coverage and bounding box (geographical)

In some cases kind of instrument ID that acquires the data

Contact information of the data center that assembles the data

Acknowledge cite

Licensing and distribution statements";Mostly. There are some metadata schemas at an acceptable level of maturity. The problem is the method to follow to ensure that metadata is correctly assigned. ;yes;"scientific publications;datasets;software;methods";;"DOI;Handle";;To provide a persistent identifier to use and, more importantly to having a strong metadata set attached to the resource. It is not only a way to cite properly a digital resource, but to embed IDs in process workflows in a reliable way.;"scientific publications;datasets;software;methods;semantic artefacts (vocabularies data models or, concepts);funders;researchers;research organisations;infrastructures";;I think that an effort mus be made to enhance discoverability, since many times, no formal ID is used, but a informal text representing the object. Probably training on these concepts will leverage the use of these technologies and methods.;yes;partly;yes;CF conventions, Essential Ocean Variables, NERC vocabularies, SeaDataNet metadata system, DataCite schema;no;The answer is mostly. Many concepts are well represented, but maybe some others no. And again, training oh how to use and select them is critical.;I try to use well community accepted ones, which in turn are the most mature.;Through on line catalogues, and then caching them in in-house database for re-use.;;"SKOS;RDF;XML";;Usually, open.;yes;Since they mature systems, they have these processes well defined I guess. Usually versioning is well defined. ;partly;I'm not pretty sure, but I think that a linked data strategy should be formulated to ensure interoperability between already mature vocabularies.;;;partly;For instance, NERV vocabularies does, but CF (as far as I know) does not.;no;;yes;Yes, made public;We have implemented a pilot process which includes Zenodo and GitHub integration, including releasing. But it is not well established yet. But we do use for instance, semantic versioning, and we are planning to have at least consistent and permanents URIs.;I guess lack of cataloguing and discoverability.;In this case, I think that the Zenodo system for properly citing software is not still part of the accepted methods of the research community. I think training is essential.;yes, please;
"ENVIRONMENT;PHYSICAL SCIENCES & ENGINEERING;COMPUTING & RESEARCH INFRASTRUCTURES;313-01 Atmospheric Science;313-02 Oceanography;315-01 Geophysics;316-01 Geochemistry, Mineralogy and Crystallography";;"Research support staff;Repository staff;Research infrastructure operator";;"ACTRIS;PRACE;Other";IS-ENES;Research infrastructure;;Spain;500-1000;"CF-1.7 

CMIP6.2";25 - 50%;75 - 100%;"Example from an ESGF data published.



		:Conventions = ""CF-1.7 CMIP-6.2"" ;

		:activity_id = ""CMIP"" ;

		:branch_method = ""none provided"" ;

		:branch_time = 0. ;

		:branch_time_in_child = 0. ;

		:branch_time_in_parent = 0. ;

		:contact = ""cmip6-data@ec-earth.org"" ;

		:creation_date = ""2019-03-10T12:50:10Z"" ;

		:data_specs_version = ""01.00.27"" ;

		:experiment = ""all-forcing simulation of the recent past"" ;

		:experiment_id = ""historical"" ;

		:external_variables = ""areacella"" ;

		:forcing_index = 1 ;

		:frequency = ""mon"" ;

		:further_info_url = ""https://furtherinfo.es-doc.org/CMIP6.EC-Earth-Consortium.EC-Earth3.historical.none.r7i1p1f1"" ;

		:grid = ""ORCA1T255"" ;

		:grid_label = ""gr"" ;

		:initialization_index = 1 ;

		:institution = ""AEMET, Spain; BSC, Spain; CNR-ISAC, Italy; DMI, Denmark; ENEA, Italy; FMI, Finland; Geomar, Germany; ICHEC, Ireland; ICTP, Italy; IDL, Portugal; IMAU, The Netherlands; IPMA, Portugal; KIT, Karlsruhe, Germany; KNMI, The Netherlands; Lund University, Sweden; Met Eireann, Ireland; NLeSC, The Netherlands; NTNU, Norway; Oxford University, UK; surfSARA, The Netherlands; SMHI, Sweden; Stockholm University, Sweden; Unite ASTR, Belgium; University College Dublin, Ireland; University of Bergen, Norway; University of Copenhagen, Denmark; University of Helsinki, Finland; University of Santiago de Compostela, Spain; Uppsala University, Sweden; Utrecht University, The Netherlands; Vrije Universiteit Amsterdam, the Netherlands; Wageningen University, The Netherlands. Mailing address: EC-Earth consortium, Rossby Center, Swedish Meteorological and Hydrological Institute/SMHI, SE-601 76 Norrkoping, Sweden"" ;

		:institution_id = ""EC-Earth-Consortium"" ;

		:mip_era = ""CMIP6"" ;

		:parent_activity_id = ""CMIP"" ;

		:parent_experiment_id = ""piControl"" ;

		:parent_mip_era = ""CMIP6"" ;

		:parent_source_id = ""EC-Earth3"" ;

		:parent_sub_experiment_id = ""no parent"" ;

		:parent_time_units = ""days since 1850-01-01"" ;

		:parent_variant_label = ""r0i1p1f1"" ;

		:physics_index = 1 ;

		:product = ""model-output"" ;

		:realization_index = 7 ;

		:realm = ""atmos"" ;

		:source = ""EC-Earth3 (2018): \n"",

			""aerosol: none\n"",

			""atmos: IFS cy36r4 (TL255, linearly reduced Gaussian grid equivalent to 512 x 256 longitude/latitude; 91 levels; top level 0.01 hPa)\n"",

			""atmosChem: none\n"",

			""land: HTESSEL (land surface scheme built in IFS)\n"",

			""landIce: none\n"",

			""ocean: NEMO3.6 (ORCA1 tripolar primarily 1 deg with meridional refinement down to 1/3 degree in the tropics; 362 x 292 longitude/latitude; 75 levels; top grid cell 0-1 m)\n"",

			""ocnBgchem: none\n"",

			""seaIce: LIM3"" ;

		:source_id = ""EC-Earth3"" ;

		:source_type = ""AOGCM"" ;

		:sub_experiment = ""none"" ;

		:sub_experiment_id = ""none"" ;

		:table_id = ""Amon"" ;

		:table_info = ""Creation Date:(20 July 2018) MD5:0d0b5611749b4875d48380f39acaca19"" ;

		:title = ""EC-Earth3 output prepared for CMIP6"" ;

		:tracking_id = ""hdl:21.14100/1b675682-9682-4114-b9df-8bb634c47c27"" ;

		:variable_id = ""tas"" ;

		:variant_info = ""forcing: Nat.Ant. Member generated from autosubmit member fc0"" ;

		:variant_label = ""r7i1p1f1"" ;

		:license = ""CMIP6 model data produced by EC-Earth-Consortium is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (https://creativecommons.org/licenses). Consult https://pcmdi.llnl.gov/CMIP6/TermsOfUse for terms of use governing CMIP6 output, including citation requirements and proper acknowledgment. Further information about this data, including some limitations, can be found via the further_info_url (recorded as a global attribute in this file) . The data producers and data providers make no warranty, either express or implied, including, but not limited to, warranties of merchantability and fitness for a particular purpose. All liabilities arising from the supply of the information (including any liability arising in negligence) are excluded to the fullest extent permitted by law."" ;

		:cmor_version = ""3.4.0"" ;

		:nominal_resolution = ""100km"" ;

		:history = ""Wed Jul 24 20:15:16 2019: ncatted -O -a nominal_resolution,global,m,c,100km ./CMIP/EC-Earth-Consortium/EC-Earth3/historical/r7i1p1f1/Amon/tas/gr/v20190302/tas_Amon_EC-Earth3_historical_r7i1p1f1_gr_190001-190012.nc\n"",

			""Sun Jun 16 09:29:40 2019: ncatted -O -a calendar,time,m,c,gregorian /esarchive/exp/ecearth/a1st/cmorfiles/CMIP/EC-Earth-Consortium/EC-Earth3/historical/r7i1p1f1/Amon/tas/gr/v20190302/tas_Amon_EC-Earth3_historical_r7i1p1f1_gr_190001-190012.nc\n"",

			""2019-03-10T12:43:09Z ; CMOR rewrote data to be consistent with CMIP6, CF-1.7 CMIP-6.2 and CF standards.;\n"",

			""processed by ece2cmor v{version}, git rev."" ;

		:NCO = ""4.7.2"" ;";Yes;yes;"scientific publications;datasets;files containing metadata;semantic artefacts (vocabularies, data models, concepts)";;DOI;;For data provenance.;"scientific publications;datasets;files containing metadata;software;semantic artefacts (vocabularies data models or, concepts)";;;no;yes;yes;"MIP tables (https://github.com/PCMDI/cmip6-cmor-tables).

GRIB tables (https://apps.ecmwf.int/codes/grib/format/grib2/ctables/)

WMO ";yes;;Comunity decision.;Websites or control version systems.;;other;JSON;;yes;Governing bodies or committees.;no;Community specific for individual use.;CF conventions: http://cfconventions.org/;Don't know.;"I don't know";;yes;Some contributions to CMIP tables for seasonal runs.;yes;Yes, made public;Using Gitlab (https://earth.bsc.es/gitlab) software is released. We don't have persistent identifiers.;Not all software is easy available through the web.;"Lack of documentation. 

Portability to other platforms.

Evaluation and replication of results.

Deprecation of versions.";yes, please;
"HEALTH & FOOD/ LIFE SCIENCES";;Research support staff;;;;University;;Other European country;"1000<";There are no official recommendations. Researchers don't have any association with  metadata standards. The institutional repository uses a small subset of DataCite fields;"<10%";"<10%";There are almost no published datasets in the community where I work;Data publication is hardly a thing in my community. Therefore there is very little I can say about metadata standards. For most researchers these words don't ring a bell;no;;;;;;;;Again, very little is done for data publication, even the metadata from the studies is hardly ever published. Therefore there is little/no discussion of persistent identifiers. However, there is a need for sustainable identification of the data, especially for dinamic datasets and databases that are being updatted over the time;;;no;I couldn't find any recommendations;;;;;;;;;;;;;;;;;;;yes;Yes, made public;It is usually published on github. The institutional repository is not well suited for software publication;I don't know;I don't know;yes, please;
"HEALTH & FOOD/ LIFE SCIENCES";;Research infrastructure operator;;INSTRUCT ERIC;;Research infrastructure;;United Kingdom;"<100";Due to the diverse nature of the science and scientific datasets that are used no metadata standards are enforced by us as a research infrastructure. However, within a number of very experiment-centric areas, such as Cryo-EM, there are emergent standards for metadata. Data formats have been standardised for a long time, but accompanying metadata, its format and the storage location continues to be a challenge.;25 - 50%;"<10%";;;no;;;;;;;;PIDs are requested regularly in our community for a number of situations, from linking identifiers to samples, sessions, software and even configurations but this is very new and not something that is robustly addressed at all yet.;;;no;;;;;;;;;;;;;;;;;;;;yes;Yes, with selected parties only;"To clarify:



Within our institute, Instruct-ERIC Hub, the tools we produce are made available through a cloud SaaS model.



However, within our research infrastructure we have a huge number of bioinformatitions producing tools that are versioned and released. Versions are not associated with PIDs at all (to my current knowledge) for any of the tools being produced in the structural biology.";;;yes, please;
"HEALTH & FOOD/ LIFE SCIENCES";;Research support staff;;;;University;;Finland;500-1000;National Library of Finland knows better;;;;;"I don't know";;;;;;;;;;;yes;YSO, MeSH;no;The Finnish language;it should be ontologized;see 3a - the problems of translations;Good question - I should go and ask them!;SKOS;;;"I don't know";;partly;some thesauri are not ontologized totally (I think);"The National Library of Finland is responsible

the Finto team

My interest is to analyze how well e.g. Finto is working in a special field";Finto-team knows;"I don't know";;yes;FinMeSH;yes;Yes, within institute only;;;;yes, please;
"HEALTH & FOOD/ LIFE SCIENCES";;Researcher;;FAIR;;University;;Netherlands;"1000<";"Focus largely in health and biomedical terminologies: DRGs (DBC in Dutch), ICD-10, SNOMED CT.

A growing interest in the application of clinical information models, which describe what data to collect in what way. No true standards for that yet, although much is based on ISO/TS 13972:2015 - Health informatics — Detailed clinical models, characteristics and processes.

Little use of others, maybe some Dublin Core here and there, but not widely accepted and used, afaik.";50 - 75%;10 - 25%;A data dictionary;"I guess not, otherwise they would have been applied more and better. Little (formal) use of Dublin Core and things like that. Probably also lack of support / enforcement to adopt such standards.

";"I don't know";;;;;;;;I think they are, but they are probably known too little to be used widely.;;;yes;DRGs (DBC in Dutch), ICD-10, SNOMED CT;yes;;"In healthcare, national ""criteria"" describe what artefacts to use. In research, these are adopted, but I think there is still little selection, due to lack of knowledge, and much replication of work and use of home-grown artefacts.";Ontology lookup service, BioPortal, Google;None that I know of.;"SKOS;OWL;RDF";;Varying. Some open, some require (national) license.;partly;"Some are well-organized, such as SNOMED CT, providing versioning, clear change request procedures, inactivation of content.

Others are less clear, hard to determine changes, unclear maintenance policies, and some even seem(ed) to reuse obsolete codes.";partly;UMLS metathesaurus, OMOP vocabulary and Bioportal provide interlinking mechanisms to a number of them.;I doubt whether there is a common process. If so, I'm not aware of it.;Protege, home-grown tooling;"I don't know";;yes;SNOMED CT;no;;;;;yes, please;
"HEALTH & FOOD/ LIFE SCIENCES;201-07 Bioinformatics and Theoretical Biology;205-03 Human Genetics";;Other;Data Steward;;;Other;University Medical Center;"Latvia;Netherlands";100-500;"Dublin Core

EGA metadata standard";10 - 25%;"<10%";Sample, Experiment, and Study specific information according to the EGA upload form.;"Overviews like these help: https://rd-alliance.github.io/metadata-directory/standards/

However, the actual implementation of a specific metadata standard is challenging. Usually researcher comply to whatever ""standard"" the dedicated repository / publisher / archive demands.



New data stewardship approaches try to implement better metadata capturing, provenance tracking, and documentation writing. Which ideally would exceed the limited set of metadata one repository/archive could represent in their metadata body.";yes;"scientific publications;datasets;files without metadata;files containing metadata;software;semantic artefacts (vocabularies, data models, concepts)";;"DOI;URN";;"mainly for paper publications; ideally for data/software publications via zenodo or github as well; URN for ontology related work.";"scientific publications;datasets;files containing metadata;software;semantic artefacts (vocabularies data models or, concepts);funders;researchers;research organisations;infrastructures";;"ORCIDS and DOIs are quite common now, PIDs for infrastructures etc. not so much. There is little awareness how to interlink and refer to all kind of resources in a metadata body of a publication (e.g. via Zenodo); but with a bit of awareness raising and training the researcher adapt quickly. 



With regards to a domain specific example: EGA only applies URLs online and accession numbers, which I would not regards as PID.";"I don't know";partly;yes;"Gene Ontology (GO)

Experimental Factor Ontology (EFO)

Dublin Core (DCMI)

Data Use Ontology (DUO)

Feature Annotation Location Description Ontology (FALDO)";yes;;"Popularity of implementation / application within the domain

Quality of architecture / structure and documentation

Overlap of useful terms

Community standardisation and maintenance ";"Mainly using http://www.ontobee.org/

DUO was discovered via https://www.ga4gh.org/";None. We are currently developing a RDF based and SPARQLing supported platform for our institute called 'SPARQLing Genomics'. Ideally this platform helps our researchers to ingest and transform their data into standardised RDF. (And later query on the knowledge graph.);"OWL;RDF";;We are currently considering the Creative Commons Suite for some parts of the exportable output, and GNU GPL for the RDF and SPARQL set-up.;yes;There is no development and matured policy yet. However, we integrated check-sums and URNs for every RDG triple part. It is intended that every single entity has their own unique PID, that is versioned as well.;yes;;We currently work with RDF triplets and the SPARQL protocol to enable querying in the RDF triple store.;"With regards to this specific project: 

vcf2rdf

bam2rdf

table2rdf

json2rdf

xml2rdf

folder2rdf

sg-web ";yes;Ontology description;yes;customised ontologies terms that complete the needs for the SPARQLing Genomics portal and fills the gaps of the other applied ontologies mentioned in D.2.;yes;Yes, made public;Besides the application of GitHub and similar platforms, another (by Data Stewardship promoted) way is to facilitate Zenodo as publication platform for software since it provides all the required features.;Lack of proper/uniform description and metadata, documentation issues, paywalls or unavailability of cited software.;Licensing issue, documentation issues, implementation issues due to broken dependencies.;yes, please;
"HEALTH & FOOD/ LIFE SCIENCES;206-06 Cognitive Neuroscience";;"Research support staff;Researcher";;;;University;;"Italy;Netherlands";"1000<";BIDS (http://bids.neuroimaging.io), DataCite, Dublin Core;75 - 100%;25 - 50%;research project abstract, data dictionary, analysis scripts ;BIDS is well suited (since new and designed by researchers), others are not so suited (since older and designed by librarians).  ;yes;"scientific publications;datasets";;"DOI;Handle";;to identify specific version, to implement persistent availability over the web;"datasets;software";;"They are largely unknown to the readers, and hence it is more common to use a textual description instead of a PID (i.e. a reference to a paper without DOI, or a reference like ""software XX version y.z"",  or ""software  XX,  downloaded at 8 Aug 2019"". 



";no;partly;yes;Cognitive Atlas (http://cognitiveatlas.org/), CogPo (http://www.cogpo.org), MeSH (https://www.ncbi.nlm.nih.gov/mesh), MNI and/or Talairach template space (for neuroimaging) ;no;They are not used a lot ;Developed in a serious research endeavor, persistently available (e.g. own website rather than hosted under some institution website), ease of use.;;The recommendation is to _start_ using them ;other;human readable, pdf, websites, tabular files (excel, csv);don't know;partly;This is usually set up during the (limited) funding period of the project that initiated the development of the vocabulary, and later abandoned, or later unclear whether it is still alive. ;"I don't know";;discussion at conferences, dedicated workshop, online communist (i.e. google group and github project);github, email, google discussion, google docs;partly;versioning;yes;BIDS (bids.neuroimaging.io);yes;Yes, made public;"own website, own ftp server, own email list, github repository, daily software releases (following testing, not released on ""bad"" days), no persistent identifiers, no semantic versioning, version corresponds to the date of the release. See http://www.fieldtriptoolbox.org/development/dashboard/



";poor documentation, unclear what level of support to expect, unclear whether software is (or will be) maintained;dependencies on other software (e.g. interpreters, other libraries)  ;yes, please;
"HEALTH & FOOD/ LIFE SCIENCES;COMPUTING & RESEARCH INFRASTRUCTURES";;"Research support staff;Repository staff";;INSTRUCT ERIC;;Research infrastructure;;"France;Spain;United Kingdom;Other European country";"<100";;;;;;yes;scientific publications;;"DOI;other";ORCID, PubMedID;;"scientific publications;datasets";;"Moving forward we want to use PIDs to identify basically everything - publications, yes, but also datasets, samples, machines, organisations, machine configurations, frames of video and other research outputs, software version, etc. Basically everything that goes through the pipe.



We'd need to issue potentially millions, and crucially, be able to resolve these to both a human and machine readable version, with the ability to extend and add our own metadata. Then, we'd want to graph this data, again with our own verbs



Currently I'm not aware of a perfect fit for this";partly;no;no;We don't do this yet, but plan to (see C.6);;;;;;;;;;;;;;;;;;;no;;;;;;
"HEALTH & FOOD/ LIFE SCIENCES;COMPUTING & RESEARCH INFRASTRUCTURES";;Researcher;;FAIR;;"University;Research institution";;Spain;100-500;;75 - 100%;50 - 75%;basic materials and methods;too general a question to answer;yes;"scientific publications;datasets;protocols;semantic artefacts (vocabularies, data models, concepts)";;"DOI;PURL;other";w3id, lsid, other uris;persistent identification, metadata retrieval;"scientific publications;datasets;protocols;semantic artefacts (vocabularies data models or, concepts)";;I don't understand the question;no;no;yes;too many to list;"I don't know";;"fir for purpose; popularity";dedicated ontology search engines;too many to list;"SKOS;OWL;RDF;XML;SHACL;other";shex;various open and, unfortunately, also closed licenses;partly;;partly;;;;partly;;no;;yes;Yes, made public;Push to GitHub.  Formal releases to Zenodo, which are versioned and assigned a DOI;;decay over time.  Non-availability of versions used in publications.;no, thank you;
"HEALTH & FOOD/ LIFE SCIENCES;COMPUTING & RESEARCH INFRASTRUCTURES;201-04 Structural Biology;206-02 Cellular Neuroscience;206-04 Systemic Neuroscience, Computational Neuroscience, Behaviour";;Research support staff;;Other;none;"Research infrastructure;University;Research institution";;Other country or countries;100-500;I would like to find out a recommended standard for imaging;25 - 50%;10 - 25%;Instrument data, date, subjects data (age, gender), topic of research, time period;"the closest I've found is the BIDS 

https://bids.neuroimaging.io/";yes;"scientific publications;files containing metadata;software;methods";;"DOI;Handle;other";RAID;to link research outcomes;"scientific publications;datasets;software;methods;funders;researchers";;;partly;partly;yes;https://neuinfo.org/about/nifvocabularies;yes;;;;;"OWL;RDF";;Mostly CC by;no;;;;;;;;;;yes;Yes, with selected parties only;;;;yes, please;
HUMANITIES;;"Research support staff;Repository staff";;CLARIN ERIC;;Research infrastructure;;Finland;"<100";CMDI, META-SHARE;75 - 100%;50 - 75%;Name, shortname, PID, license, description, relations;yes.;yes;"datasets;metadata records";;"DOI;URN;Handle";;PIDs are mandatory for citation, nice to have for licenses, dataset locations.;metadata records;;yes;no;yes;"I don't know";;;;;;;;;;;;;;;;;;;;yes;Yes, made public;Software is published similar to data, with metadata PIDs, versions, etc.;;;yes, please;
HUMANITIES;;Research support staff;;DARIAH ERIC;;Research institution;;France;"1000<";TEI, cidoc-crm, dublin core;"<10%";"<10%";dublin core;TEI, EAD are standards with rich metadata. The TEI is very well suited for the community.;yes;"scientific publications;datasets;software;semantic artefacts (vocabularies, data models, concepts)";;"DOI;URN;Handle;ARK";;identification and persistent access;"scientific publications;datasets;metadata records;semantic artefacts (vocabularies data models or, concepts);researchers";;;yes;no;yes;CIDOC-CRM, Pactols (archeology);no;Because researcher are were not trained to the base skill of designing controlled vocabularies. Even FRBR is difficult for them to understand, because it require to think about heritage artifacts in a more abstract way than the one they were trained to use.;It depends, I don't understand the question;same;Develop modelling skills to be able to align vocabularies;"SKOS;RDF;XML";;CCBY, CCBY SA, it depends of the intellectual property attached to each artefact...;no;;"I don't know";;Extract metadata, use a thesaurus, align vocabularies, export data sets from data bases to populate sparql endpoints or disciplinary portals.;Open Theso, protege,;"I don't know";;no;I contribute in working with TEI, trying to anticipate need for re-use of (meta)data;yes;Yes, made public;Github/gitlab publishing;Finding software is one thing, being able to install it, use it properly, debug, and integrate in the researchers existing workflows or platform requires time and skill, so to say support IT staff.;same;yes, please;
"PHYSICAL SCIENCES & ENGINEERING";;Repository staff;;;;Other;Disciplinary Data Repository;United Kingdom;"<100";Crystallographic Information Framework (CIF);75 - 100%;75 - 100%;"Descriptions of sample being studied

Information about equipment used and experimental conditions

Details of methods used and parameters applied

Information about software packages used

Quality measures

";Yes.;yes;"scientific publications;datasets";;"DOI;other";Database Accession IDs;Identifiying, citing and linking to research objects;"scientific publications;datasets;researchers";;Now we are getting clarity around organisational identifiers, largely yes. I think it will take a while before we can reliably join up all actors and objects involved in a research output though.;no;yes;yes;CIF;yes;;Instrument and data analysis software uses whetver artefacts are most approriate. Researchers may choose to use additional ones. Repositories augment with audit, citation and other artefacts.;Via the data file;Get instruments, software and repositories to do this for the researcher so they don't have to.;other;CIF;Openly available;yes;The International Union of Crystallogtraphy (IUCr) has committees dedicated to maintenance of the CIF standard;"I don't know";;IUCr COMMCIF receive or generate recommendations that are then circualted for comment amongst experts.;CIF/STAR;yes;CIF Dictionary defines all terms;no;;yes;Yes, made public;We run a professional software development activity as part of our operations that results in periodic releases of software, each with new version numbers.;Don't know.;Don't know.;no, thank you;
"PHYSICAL SCIENCES & ENGINEERING";;Repository staff;;;;Research institution;;Germany;"1000<";;10 - 25%;10 - 25%;"Funding information

Information on Author

Information on first publication

keywords and classifiaction

abstract

technical information";some institution-specific metadata for statistics and promotion is not covered by a standard;yes;"scientific publications;datasets";;"DOI;URN;Handle";;Persistent Identification, Accessibility;"scientific publications;datasets;software";;so far they are.;no;yes;yes;"ISO-Standard for Language

Dewey Decimal Classification";no;DDC is not convient for all of our research topics. It is not up-to-date enough.;"easy access

high usage

up-to-date

strong community behind standard

cerficition for example ISO";;;;;;"I don't know";;"I don't know";;;;no;;no;;yes;Yes, with selected parties only;;;;no, thank you;
"PHYSICAL SCIENCES & ENGINEERING";;"Research support staff;Research infrastructure operator";;EISCAT_3D;;Research infrastructure;;Sweden;"<100";Community metadata;"<10%";"<10%";PI, Software+vs, Hardware used;Yes;no;;;;;;;;Yes;;;no;None;;;;;;;;;;;;;;;;;;;yes;Yes, made public;"Own git repo

Software+version written to the data";Only a handful is available;Too hardware specific;yes, please;
"PHYSICAL SCIENCES & ENGINEERING;309-01 Nuclear and Elementary Particle Physics, Quantum Mechanics, Relativity, Fields;310-01 Statistical Physics, Soft Matter, Biological Physics, Nonlinear Dynamics";;"Researcher;Other";stakeholder;PRACE;;"Research infrastructure;Research institution";;Cyprus;100-500;Metadata standards are not being used in my community. Nevertheless, in the project I represent several metadata standards are being used depending on the topic such as Dublin Core, CF, etc;"<10%";"<10%";Metadata regarding the algorithmic and physical  details of the datasets.;There are no metadata standards available for my community. There should be a dedicated study towards this direction.;yes;"scientific publications;datasets;software";;DOI;;To identify publications and datasets and link them to the web;"scientific publications;datasets";;Yes the available identifiers are well suited for my community and the purpose I want to use them for.;yes;yes;no;No vocabularies and/or ontologies are recommended to be used in my community.;;;;;;;;;;;;;;;;;;;yes;Yes, made public;Depending on the software and the agreement with the institution, if a software is expected to be openly accessible, this is achieved by uploading it to github which provides versioning, persistent identifiers and metadata.;No good onotological solutions exists which can provide interoperability between different thematic branches.;Lack of how to use the software, bad documentation, lack of workflows.;yes, please;
"PHYSICAL SCIENCES & ENGINEERING;408-02 Communications, High-Frequency and Network Technology, Theoretical Electrical Engineering";;Researcher;;;;University;;Finland;"1000<";there are no recommended standards;;;type, format, intended use cases;I don't know of any standards;yes;datasets;;DOI;;Fro referencing in other publications;;;;no;"I don't know";no;;;;;;;;;;;;;;;;;;;;no;;;;;no, thank you;
"PHYSICAL SCIENCES & ENGINEERING;COMPUTING & RESEARCH INFRASTRUCTURES";;Research support staff;;"SKA;PRACE";;University;;Netherlands;"1000<";;25 - 50%;50 - 75%;;;"I don't know";;;;;;;;;;;"I don't know";;;;;;;;;;;;;;;;;;;;yes;Yes, with selected parties only;;;;no, thank you;
"PHYSICAL SCIENCES & ENGINEERING;COMPUTING & RESEARCH INFRASTRUCTURES;313-01 Atmospheric Science;313-02 Oceanography;409-08 Massively Parallel and Data-Intensive Systems";;Policy maker;;Other;IS-ENES;Research infrastructure;;Germany;"<100";"NetCDF/CF (standard for use of community format)

project standards widely used

DataCite

ISO19115";50 - 75%;"<10%";"Background information on data creation and contacts; most of the information (use metadata) is part of the self-describing file format NetCDF/CF.

(Remark for metadata added to datasets: It is not common to publish the datasets but if it is done they are published with metadata.)";Community standards are well suited as developed in a botton-up process and supported by tools. Same for specific metadata like citation metadata (DataCite). More general and larger standards like ISO19115 are partly difficult to adjust.;yes;"scientific publications;datasets;other";data collections (high-volume data DOI);"DOI;Handle;other";additionally short URLs are widely used for less important metadata parts;"Data Citation, Data Identification, plans for Software, Data Products and Provenance Records;

of cause we also use common identifiers for researchers, funders and research organizations (ORCID, ISNI, CrossRef FunderID, ROR)";"scientific publications;software;funders;researchers;research organisations;other";Data Collections (DOIs);Yes, with a problem in using some of the available measures because of the DOIs on data collections, where the tools assume DOIs or PIDs on datasets.;yes;partly;yes;project naming / data structure conventions like Data Reference Syntax;yes;;For organization of data published on different sites of a federated infrastructure - ensure uniqueness and have meaningful short names;Projects refer to existing community standards and add/collect additional ones.;;"XML;other";JSON (because of easy machine-access);none;partly;github tracking of changes sometimes explicit version in the file;partly;Large projects reuse parts of what worked but tend to adapt. Usually a infrastructure contact is included into the discussion to grant a common part.;Project-driven: Large international projects are very influential. These project approaches tend to become community standards.;"divers tools used for discussion of content; one responsible person brings it into a usable format";yes;Documentation available as separate document and attached to the artifact but not standardized.;yes;Technical contact and/or contact for curation / long-term aspects;yes;;"Numeric modeling has many layers of ""software"": models are usually developed in international collaborations between different institutions. Analysis software packages are shared with open licenses. For individual post-processing and analysis there is a move towards publishing them more often. ";;"Numeric models: set-up on specific platform, building knowledge to apply, input data,...

Analysis software: researchers are numeric modelers and usually have no problems to install software.";no, thank you;
"PHYSICAL SCIENCES & ENGINEERING;SOCIAL SCIENCES";;Research support staff;;"BBMRI ERIC;FAIR;CESSDA ERIC";;University;;Netherlands;"1000<";DDI for the social scientists. Otherwise Dublin Core.;10 - 25%;"<10%";Only the information required when depositing in DataverseNL, DANS or on OSF;"Yes, BUT:

Many researchers are lost on how they are supposed to generate this for themselves, particularly machine-readable metadata. If researchers go to the DDI page it is not immediately apparent how to use DDI. So they get lost and frustrated easily.";"I don't know";;;;;;;;Where data is being deposited in trusted repositories, then they are using PIDs. Not everyone is depositing data yet however. Many researchers are worried about GDPR restrictions. At this point we are just trying to sort out a lot of logistics at our institution and make researchers aware of where and how they can deposit their data for publication.;;;"I don't know";I am not sure about this area for either social sciences or movement sciences. I will look into it.;;;;;;;;;;;;;;;;;;;yes;Yes, with selected parties only;I think the aim is to work towards publishing some software being produced, but we aren't that far along yet.;Not sure if they are allowed to use it.;See above.;yes, please;
SOCIAL SCIENCES;;Repository staff;;CESSDA ERIC;;"Research infrastructure;University";;Finland;;"DDI (Data Documentation Initiative)

See also SSHOC D3.1: https://sshopencloud.eu/d31-sshoc-report-sshoc-data-interoperability-problems";25 - 50%;10 - 25%;Information on methodology and data collection.;Yes, DDI is designed for social sciences.;yes;"scientific publications;datasets";;"DOI;URN";;To be able to cite datasets and publications.;scientific publications;;;no;yes;yes;Many, for example DDI Alliance CVs;yes;;They have to be fit for purpose. Multilinguality is a plus.;;CESSDA has recommendations on metadata. CESSDA also has a CV Service tool: https://vocabularies.cessda.eu;SKOS;;CC BY 4.0;yes;https://ddialliance.org/controlled-vocabularies;partly;This varies a lot.;;;yes;;no;;yes;;;;;no, thank you;
SOCIAL SCIENCES;;Research support staff;;;;University;;Other country or countries;500-1000;Dublin Core;10 - 25%;"<10%";;;;;;;;;;;;;;no;;;;;;;;;;;;;;;;;;;;no;;;;;yes, please;
"SOCIAL SCIENCES;112-03 Business Administration;409-06 Information Systems, Process and Knowledge Management";;Research support staff;;;;University;;Germany;"1000<";"METS

MODS

JSON-LD

";"<10%";"<10%";;;yes;"scientific publications;software";;DOI;;;"scientific publications;software;researchers";;;no;partly;no;;;;;;;;;;;;;;;;;;;;yes;Yes, made public;GitHub => Zenodo;;;no, thank you;
"SOCIAL SCIENCES;COMPUTING & RESEARCH INFRASTRUCTURES";;"Repository staff;Research infrastructure operator";;;;University;;United Kingdom;"<100";"DDI-Codebook (http://www.ddialliance.org/Specification/DDI-Codebook/2.5/)

DDI-Lifecycle (http://www.ddialliance.org/Specification/DDI-Lifecycle/3.2/)

Dublin Core



";75 - 100%;75 - 100%;Full description of variables, variable statistics, and missing values;Yes;yes;"datasets;files containing metadata;semantic artefacts (vocabularies, data models, concepts)";;"DOI;URN";;Identification of all metadata elements and datasets  ;"datasets;semantic artefacts (vocabularies data models or, concepts)";;;yes;yes;yes;"DDI Controlled Vocabularies (http://www.ddialliance.org/controlled-vocabularies)

ISO-3166

ICD10 (and previous versions)

Office for National Statistics Classifications 

MESH

HASSET (https://lod.data-archive.ac.uk/v2-skoshasset/page/en-GB/)";yes;;Community acceptability;;;"SKOS;XML";;"CC-BY-SA

";yes;"DDI Controlled Vocabularies has a community driven process (http://www.ddialliance.org/system/files/DDIAllianceStandardsDevelopmentandReviewProcessandProcedure.pdf) 

";"I don't know";;;;yes;ISO-11179 compliant e.g. https://www.ddialliance.org/Specification/DDI-CV/AggregationMethod_1.0.html;yes;"DDI Controlled Vocabulary

";yes;Yes, made public;"We use GitHub to publish the code base of our software at CLOSER-Cohorts/archivist. This is used for metadata curation.

We also use commercial software, Colectica Repository (https://www.colectica.com/software/repository/) and Portal (https://www.colectica.com/software/portal/) for management, version control, PIDS etc. Version control management is done using DDI Best Practices (http://www.ddialliance.org/system/files/DDI%203.2%20Best%20Practices_0.pdf) 







";;Interoperability of the content in the metadata standards;yes, please;
"SOCIAL SCIENCES;HUMANITIES";;"Repository staff;Research infrastructure operator";;CESSDA ERIC;;"Research infrastructure;University";;Finland;"<100";"Primary DDI (Data Documentation Initiative) 

Secondary: DC, EAD, METS";75 - 100%;10 - 25%;Data collector, time period, universe, sampling method;Yes, DDI suits our needs very well. ;yes;"datasets;metadata records";;"DOI;URN";;Mostly for identifying the landing page of the dataset in a repository;"scientific publications;datasets;researchers";;For the current level of use they are sufficient. If the plan would be to build more heavily on them, some questions may arise. ;partly;partly;yes;DDI Controlled Vocabulary, ELSST, YSA/YSO;yes;;They must be aligned with community standards and interoperable with the research infrastructure on the international level.;Using national and international vocabulary services specific to our needs/field.;Common vocabulary service. ;SKOS;;Creative Commons Attribution 4.0 International;yes;;yes;;;;yes;;yes;DDI, ELLST;yes;Yes, made public;;;;yes, please;
"SOCIAL SCIENCES;HUMANITIES;102-01 Medieval History;102-02 Early Modern History;102-03 Modern and Current History;103-01 Art History;103-02 Musicology;103-03 Theatre and Media Studies;104-04 Applied Linguistics, Experimental Linguistics, Computational Linguistics";;"Research support staff;Research infrastructure operator";;;;University;;"Latvia;Netherlands";"1000<";"By whom?

Anyway: DDI & DC";10 - 25%;10 - 25%;Our own metadata scheme, consisting of 24 elements, of which 8 are mandatory;Yes, they are for describing an archived data package. However for a description of the data it is suboptimal, hence we request for a codebook to be stored with the data.;yes;"scientific publications;datasets;files without metadata;metadata records";;"DOI;Handle;other";EPIC;See answer C.2;"scientific publications;datasets;researchers";;Yes;no;yes;yes;"We currently use:

- Scientific disciplines: the OECD list (http://www.oecd.org/science/inno/38235147.pdf)

- Languages: ISO 639/1

";no;"The OECD discipline list is biased toward Social Sciences and Sciences, not so much to the humanities.

Another issue is the availability: currently we have the lists replicated localy, which bring along issues with maintainability.

";Continuity of backing organization, reputation of the vocabulary, relevance.;Google, peers;We replicate them locally so that we're not dpending on external services being up.;"OWL;RDF;XML";;I don't understand this question (we only use artefacts from the public domain);no;;"I don't know";;Currently none;Currently none;no;;no;None;yes;Yes, within institute only;Informal process;"How does it work in detail

How to get it installed and hosted

Where to find how-to's ";"How does it work in detail

How to get it installed and hosted

Where to find how-to's ";yes, please;
"SOCIAL SCIENCES;HUMANITIES;COMPUTING & RESEARCH INFRASTRUCTURES";;"Research infrastructure operator;Researcher";;"CLARIN ERIC;DARIAH ERIC";;University;;Czechia;"1000<";AOI-PMH for exchange, DC and CMDI formats.;25 - 50%;10 - 25%;"It depends on the publishing platforms. A lot of data is still published outside repositories, on random web pages of authors, projects, github.io, etc.



In our repository it is licensing, domain (language data) specific, full provenance record, and more.";yes they are. The problem is that the repositories are under-used, but not because they would be unsuitable. ;yes;"scientific publications;datasets;software";;"DOI;Handle";;reliable reference. In citations and elsewhere.;"datasets;software";;yes, they are well suited. Problem is that nobody knows Handles and i.e. citation formats often require DOIs.;partly;yes;no;;;;;;;;;;;;;;;;;;;;yes;Yes, made public;public version control systems, repository records for versions that are used for significant tasks, e.g. processing a published dataset.;sharing models needed to run the software, due to copyright and licensing problems with training data.;sometimes lack of APIs to process larger data. Not in our infrastructure, though.;no, thank you;
"SOCIAL SCIENCES;HUMANITIES;COMPUTING & RESEARCH INFRASTRUCTURES;205-26 Cardiothoracic and Vascular Surgery";;Research infrastructure operator;;"CESSDA ERIC;CLARIN ERIC;DARIAH ERIC;ESS ERIC;SHARE ERIC";;Research infrastructure;;Other country or countries;100-500;SSH Recommendations are contained in the SSHOC deliverable https://sshopencloud.eu/d31-sshoc-report-sshoc-data-interoperability-problems;50 - 75%;25 - 50%;Varies across the SSHOC recommended metadata standards but will usually include some provenance information, methodology, collection method observation units and relevant temporal and geographic metadata. ;Basic metadata standards suitable for common resource discovery systems (DC, DataCite, OpenAire) necessarily leave out the domain-specific metadata details which are necessary for specialist resource discovery and reuse. See deliverable for details of their application. ;yes;"scientific publications;datasets;files without metadata;files containing metadata;software;metadata records;semantic artefacts (vocabularies, data models, concepts)";;"DOI;URN;Handle;ARK;PURL";;data and metadata object identification (supporting resource discovery and citation);"scientific publications;datasets;files without metadata;files containing metadata;software;metadata records;semantic artefacts (vocabularies data models or, concepts);funders;researchers;research organisations;infrastructures";;As with all areas of metadata practice, there is room for wider adoption and improvement in practice.  The broad range of the ERICs in SSHOC means that most types of object are assigned identifiers and used in metadata/object cross-linkage. The respondent is not familiar with particular examples of PID assignment for methods and protocols, but they may exist. ;partly;partly;yes;"CESSDA - CESSDA Topic Classification, DDI Controlled Vocabularies, ELSST

CLARIN - CLARIN Concept Registry, CLAVAS, ISO 639-1 language list, local vocabularies

DARIAH - GND (Gemeinsame Normdatei), OpenGeoNames, TADIRAH, TGN (Getty Thesaurus of Geographic Names)

E-RIHS - AAT (Art and Architecture Thesaurus), PICO Thesaurus, TGN, VIAF (Virtual Authority File)

ESS - DDI Controlled Vocabularies (subset), ESS’ own self-defined CVs

Further details in the SSHOC deliverable.";yes;;"Mandated by funders, organisations or ERICs

Community approval/demand

Quality (completeness, etc)

Ease of use (formats, supporting technology etc)

Well managed (curated, versioned etc)";Through interacting with other community members. ;To avoid developing local solutions when standardised solutions already exist. To share any local solutions for adoption by others. To be as granular as possible (depending on resources available). To pick standards which augment comparability and interoperability of resources. ;"SKOS;OWL;RDF;XML;SHACL";;Licences range from CC0 to bespoke agreements. ;partly;Practice varies but a managed process of designing, communicating and implementing change is increasingly common as it is important for interoperability. ;partly;"Two controlled vocabularies in SKOS aren't;'t necessarily 'interoperable' even though they can both be edited with Skosmos.  So it depends on the understanding o  the term (syntactic, semantic etc). Metadata has similar issues as to schema's in XML can have very different purposes. And even within DDI metadata two different organisations or tools might use very different subsets of the elements (profiles). ";Broadly speaking: identify a need for a CV or metadata standard, consult the community over whether one exists which can be adopted or adapted or if one needs to be created, develop, test, iterate, deploy, manage (including versions over time). ;"Metadata editors like Oxygen for XML

SKOS editors like Skosmos



";partly;limited use of persistent identifiers for controlled vocabularies. ;yes;SSHOC Community members work on a range of metadata standards, CV and thesauri including CMDI, DDI, DDI CVs (to be managed through the CESSDA ERIC) and the ELSST (English Language Social Science Thesaurus. ;yes;;"These vary across the software and tools. 

https://www.dariah.eu/tools-services/tools-and-services/

https://www.clarin.eu/content/clarin-software-github

https://www.europeansocialsurvey.org/data/

https://www.share-datadocutool.org/

https://www.cessda.eu/Tools-Services



";The lack of centralised registries mapped to the purpose of the software and clear information about the level of support and documentation available. ;Low levels of support and documentation. Lack of clarity on licensing. ;yes, please;