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

Core and denotes an extended Dublin Core extending or refining the 15 core elements. We also considered Pan-MD, a metadata schema developed by PANGAEA. It extends Dublin Core with more fine-grained geographic information such as bounding boxes or adds information on data collection. The latter can range from projects, parameters, methods, and sensors to taxonomy or habitats. MARC21, MARCXML and METS are metadata standards that are mainly used for biblio- graphic data in digital libraries. Hence, we left them out of our further explorations. We also did not consider the Common European Research Information Format (CERIF) and OAI-ORE as they are not focused on describing primary data but research entities and their relationships and grouping web resources, respectively. However, we decided to permit all available reposi- tory-developed schemata for the Life Sciences, such as Pan-MD, in order to get an impression how repositories extend metadata descriptions. RDF is not a standard but a semantic format. We decided not to omit it as it indicates the usage of semantic formats at data repositories. The metadata fields used in RDF format are mainly based on Dublin Core. Data processing. Per metadata file we inspected which elements of the metadata stan- dards are used, and we saved their presence (1) or non-presence (0). The result is a csv file per metadata standard containing dataset IDs and metadata elements used. All generated files are stored in separate folders per repository and metadata standard. Each request to a repository

returns an XML body that includes several metadata files as records. Each record is separated in two sections, a header and a metadata section. The header section comprises general infor- mation such as a unique identifier of the item and a date stamp. The metadata section contains the metadata structure, e.g., the name of the contributors, abstract and publication year. Unused metadata fields are not included in the response. We saved a boolean value encoding whether a metadata field was used or not. The source code and documentation on how to use it is available in our GitHub repository. For our further consideration, we wanted to obtain a publication date of each downloaded dataset to inspect how many datasets have been published over the years in which standard per data repository. Unfortunately, a publication date is not provided in all metadata schemata. Therefore, we looked up each date related field in the schema and used the one that is (based on the description) the closest to a publication date. Table 5 depicts all date stamps utilized and their descriptions. If the respective date stamp was not found in a dataset or was empty, we left the dataset out in the following analysis. Data collection for content analysis. General, descriptive metadata fields such as ‘title’, ‘description’ or ‘abstract’, and ‘subject’ might contain relevant data that are interesting for information seekers. Using conventional retrieval techniques, this data is only accessible in a full text search and if the entered query terms exactly match a term in the dataset. These

Table 4. Metadata schemes and formats offered by selected data repositories in their OAI-PMH interfaces. Dryad GBIF PANGAEA Zenodo Figshare METS EML DATACITE3 DATACITE CERIF OAI-DC OAI-DC DIF DATACITE3 METS OAI-ORE ISO19139 DATACITE4 OAI-DATACITE RDF ISO19139.IODP MARCXML OAI-DC OAI-DC MARC21 QDC PAN-MD OAI-DATACITE RDF OAI-DATACITE3 OAI-DC https://doi.org/10.1371/journal.pone.0246099.t004 PLOS ONE Dataset search in biodiversity research PLOS ONE | https://doi.org/10.1371/journal.pone.0246099 March 24, 2021 21 / 36