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

and Dryad reveal that both repositories host marine data. PANGAEA’s list mainly contains data parameters measured and used devices. In contrast, Dryad’s list indicates that terrestrial data are also provided. For instance, the lower ranked terms contain entries such as Insects (1296) (insects (180)) or pollination (471) (Pollination (170)). Geographic information, e.g., California (9817), also occurred in Dryad’s dc:subject field. Zenodo’s and Figshare’s key- word lists contain numerous terms related to collection data. We checked the term ‘Biodiver- sity’ in both repositories in their search interfaces on their websites. It turned out that the Meise Botanic Garden (https://www.plantentuinmeise.be) provided large collection data in Zenodo. Hence, each occurrence record counted as a search hit and got the label ‘Biodiversity’. We also discovered that Figshare harvests Zenodo data which also resulted in high numbers for Figshare and the keyword ‘Biodiversity’ (219022). In a second analysis, we investigated entity types that occur in descriptive metadata fields. As the processing of textual resources with NLP tools is time-consuming and resource-inten- sive, we selected a subset of datasets. We limited the amount to 10,000 datasets per repository. Table 9 presents the filter strategies. For PANGAEA and GBIF, we randomly selected 10,000 datasets as they are domain-specific repositories for which all data are potentially relevant for biodiversity research. For Zenodo and Figshare we used the keyword ‘Biodiversity’. Due to the

large amount of collection data in Zenodo and Figshare with the keyword ‘Biodiversity’, we are aware that this filter strategy may have led to a larger number of collection datasets included in the 10,000 selected files. For Dryad, the filter contained a group of relevant keywords as a filter with only one keyword would not have returned at least 10,000 datasets. Per data repository, we processed the selected 10,000 files with open source taggers of the text mining framework GATE [62]. Named Entities such as PERSON, ORGANIZATION and LOCATION were obtained with the ANNIE pipeline [63], ORGANISMs were extracted with the OrganismTagger [64], and further biological entities (QUALITY, PROCESS, MATERIAL Table 8. Five most common keywords and their frequencies in the metadata field dc:subject. The last row denotes the amount of files with an empty dc:sub- ject field. PANGAEA GBIF Dryad Zenodo Figshare water (201102) Occurrence (6510), occurrence (46) Temperature (16652), temperature (15916) Taxonomy (459877), taxonomy (105) Medicine (1057684), medicine (240) DEPTH (198349), Depth (71916) Specimen (3046), specimen (22) Integrated Ocean Observing System (16373) Biodiversity (458336), biodiversity (8593) Biochemistry (1015906), biochemistry (92) Spectral irradiance (175373) Observation (2425), observation (24) IOOS (16373) Herbarium (270110), herbarium (91) Biological Sciences not elsewhere classified (983829) DATE/TIME (128917) Checklist (589), checklist (43) Oceanographic Sensor Data (15015) Terrestrial (269900), terrestrial (177) Chemical Sciences not elsewhere

classified (842865) Temperature (118522), temperature (50) Plantas (368), plantas (42) continental shelf (15015) Animalia (205242), animalia (261) Biotechnology (792223), biotechnology (23978) 0 38296 15436 705730 0 https://doi.org/10.1371/journal.pone.0246099.t008 Table 9. Filter strategies used per data repository to select 10,000 datasets. The number in brackets denotes the total number of available datasets (OAI-DC standard) at the time of download (October/November 2019). PANGAEA GBIF Dryad Zenodo Figshare 10000 randomly selected (388142) 10000 randomly selected GBIF (46954) 10000 randomly with keywords: biodiversity, climate change, ecology, insects, species richness, invasive species, herbivory, pollination, endangered species, ecosystem functioning, birds (149671) 10000 randomly with keyword: Biodiversity (1457958) 10000 randomly with keyword: Biodiversity (3592808) https://doi.org/10.1371/journal.pone.0246099.t009 PLOS ONE Dataset search in biodiversity research PLOS ONE | https://doi.org/10.1371/journal.pone.0246099 March 24, 2021 27 / 36