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

There is no schema that covers all categories. Since the interests are obtained from scholars with various and heterogeneous research backgrounds, this was to be expected. Apart from HUMAN INTERVENTION, all categories are covered by different metadata standards. In particular, ISA-Tab covers most of the search interests of biodiversity researchers explicitly. The description of QUALITY information (e.g., data parameters measured) are covered by a variety of standards, e.g., ABCD, Genome Metadata, SDMX. The same applies for information on the DATA TYPE and geographic information (LOCATION). For the latter, the granularity differs between the individual standards. While standards such as ISO19115, ABCD, Genome Metadata, Data Cite offering several metadata fields for the description of geographic informa- tion, other standards only provide one metadata element, e.g., CSMD, EML, Dublin Core. Metadata elements for environmental information are provided by EML (studyAreaDe- scription), UKEOF (environmentalDomain) or CSDM (Facility). Observed or involved organisms can be described with Darwin Core, ABCD or EML but also with standards focusing on molecular data (ISA-Tab, Genome Metadata and PDB/mmCIF). However, important search preferences such as materials (including chemicals) are only explicitly supported by ISA-Tab, PDB/mmCIF, CSMD and OM. While numerous standards already support the description of research methods and instruments (METHOD), only ISA- Tab offers a metadata field (Protocol REF) to describe biological or chemical processes

(PROCESS) a specimen or an experiment is involved. Even if some categories are not fre- quently mentioned (Subsection “Results and Metrics”), such as HUMAN INTERVENTION and EVENT, they should not be neglected. Extreme weather events or incidents, e.g., earth- quakes or oils spills, might be of research interest and therefore, metadata elements should be provided to define and describe them. Widely used general standards such as Dublin Core or DataCite offer at least a general field (dc:subject, subject) that could be used to describe the identified search categories. In Dublin Core, at least one metadata field each is provided to describe geographic information, e.g., where the data have been collected (LOCATION), the type of the data (DATA TYPE), the creator and contributor (PERSON & ORGANIZATION) and when it was collected or pub- lished (TIME). However, one field is often not enough to distinguish if the provided field is for instance a collection date or publication date, or if the creator of the dataset is also the person that collected the data. In contrast, DataCite provides individual fields for publication year and the date field can be used with dateType=“Collected” to specify a collection date. The metadata field contributor can also be extended with a type to indicate whether the con- tact details belong to the data collector or the project leader. Bounding box elements are also provided to enter geographic coordinates (LOCATION). A complete generic approach is CEDAR offering generic elements to set up metadata templates in various formats (e.g., JSON,

RDF) and options for integrating controlled vocabularies or schema.org entities. Summary. Generic metadata standards such as Dublin Core or DataCite do not describe primary data sufficiently for dataset search. They cover main scholarly search interests only if general fields are used and proper keywords (in best-case using controlled vocabularies) are contained. A variety of discipline-specific standards are available that go beyond data citation aspects and cover most of the important topics for search, e.g., ISA − Tab (biomedical experi- ments), Darwin Core, ABCD (species), EML (ecology), ISO19115 (geospatial data), CSMD, PDB/mmCIF and ISA − Tab (materials). However, PROCESS is currently only explicitly cov- ered by ISA-Tab. Here, the respective research communities should consider to add elements to the standards that allow an explicit description or at least to provide general fields that allow an extension. The question that still remains to be answered is what metadata standards are actually used by data repositories. PLOS ONE Dataset search in biodiversity research PLOS ONE | https://doi.org/10.1371/journal.pone.0246099 March 24, 2021 19 / 36