Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs?

location are considered with one or several metadata fields in all standards. In order to describe the main scope of the primary data, all standards offer numerous metadata fields but differ in their granularity. While simple ones such as Dublin Core only offer fields such as title, description, format, and type, standards with more elements such as EML or ABCD even offer fields for scientific names, methods and data attributes measured. EML even allows scholars to define the purpose of the study making it the only standard that supports the Why question. Data reuse and citation also play an important role. As it is demanded by the Joint Declaration of Data Citation Principles [59] and practical guidelines for data repositories [60], all standards Table 2. Metadata standards in the (life) sciences obtained from re3data [57] and RDA metadata standards catalog [58]. The number in brackets denotes the number of repositories supporting the standard (provided in re3data). Standard Name URL Domain Semantic Format Examples Dublin Core (205) http://dublincore.org/ general research data Yes (RDF) Pangaea, Dryad, GBIF, Zenodo, Figshare DataCite (111) https://schema.datacite.org/meta/kernel-4.1/ general research data No Pangaea, Zenodo, Figshare, Radar ISO19115 (47) ftp://ftp.ncddc.noaa.gov/pub/Metadata/Online_ ISO_Training/Intro_to_ISO/workbooks/MD_ Metadata.pdf geospatial data No Pangaea, NSF Arctic Data Center, coastMap FDGC/ CSDGM (42) https://www.fgdc.gov/metadata/csdgm-standard geographic information No Dataverse, NSF Arctic Data Center

Darwin Core (28) https://dwc.tdwg.org/ biodiversity data Yes (RDF) GFBio, GBIF, VerNET, Atlas of Living Australia, WORMS EML (26) https://knb.ecoinformatics.org/external// emlparser/docs/eml-2.1.1/index.html ecological data No GBIF, GFBio, SNSB, Senckenberg, WORMS, NSF Arctic Data Center RDF Data Cube (20) https://www.w3.org/TR/vocab-data-cube/ statistical data Yes Dryad (only RDF with DublinCore) ISA − Tab (13) https://isa-specs.readthedocs.io/en/latest/index. html biological experiments Yes Data Inra, GigaDB ABCD (11) https://github.com/tdwg/abcd biological collection data Yes (ABCD 3.0 in RDF) GBIF, BioCase Network OAI − ORE (11) https://www.openarchives.org/ore/ general research data Yes (RDF) Environmental Data Initiative Repository, Dryad DCAT(9) https://www.w3.org/TR/vocab-dcat data catalogs, data sets Yes Data.gov.au, European Data Portal DIF(9) https://gcmd.nasa.gov/DocumentBuilder/ defaultDif10/guide/index.html geospatial metadata No Pangaea, Australian Antarctic Data Center, Marine Environmental Data Section CF(7) http://cfconventions.org/ climate and forecast No WORMS, NSF Arctic Data Center, coastMap SDMX (4) https://sdmx.org/ statistical data No UN Data Catalog CSMD − CCLRC (1) http://icatproject-contrib.github.io/CSMD/ scientific activities, e.g., experiments, observations, simulations Yes (OWL) Monash University Research Repository Genome Metadata (1) https://docs.patricbrc.org/user_guides/ organisms_taxon/genome_metadata.html genome data No PATRIC OME − XML https://docs.openmicroscopy.org/ome-model/6.2. 0/

biological imaging Yes (OWL) CELL Image Library, JCB Dataviewer PDBx/mmCIF http://mmcif.wwpdb.org/dictionaries/mmcif_ pdbx_v40.dic/Index/index.html 3D structures of proteins, nucleic acids, and complex assemblies No wwPDB (Worldwide Protein Data Bank) UKEOF http://www.ukeof.org.uk/schema/ environmental monitoring No UKEOF catalogue CEDAR https://more.metadatacenter.org/tools-training/ outreach/cedar-template-model general but focus on scientific experiments Yes (RDF) US National Cancer Institute’s caDSR Observation and Measurement (OM) https://www.ogc.org/standards/om observational data Yes (OWL-Lite) INSPIRE (Infrastructure for Spatial Information in Europe) https://doi.org/10.1371/journal.pone.0246099.t002 PLOS ONE Dataset search in biodiversity research PLOS ONE | https://doi.org/10.1371/journal.pone.0246099 March 24, 2021 17 / 36