Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
31
datasets available to search
ShareScore release 0.7.1
Dataset results
31 results for “Biodiversity informatics”
Figure 4 in Optimizing biodiversity informatics to improve information flow, data quality, and utility for science and society
Figure 4. Graphical representation of original and recently modified pathways for feedback regarding Primary Biodiversity Data, showing information transfer among users, providers, and aggregators. Such feedback consists of suggested improvements or additions to data fields, for example a change in species identification or a newly determined georeference. The diagrams contrast two complementary mechanisms: (a) the original feedback loop (currently dominant); and (b) the emerging feedback pendulum (proposed for expansion). In a: (1) the user sends feedback to the provider (e.g., a given natural history museum); (2) if the provider makes a corresponding change to its database, the updated information is sent to the aggregator; and (3) that information becomes available for query by all users. In practice, because many providers do not consistently make such changes (denoted by an X), users do have access to updated information (dashed line). In b: (1) the user sends feedback to the aggregator; (2) the aggregator simultaneously both annotates the record (visible to all users) and sends the suggested information to the provider; (3) if the provider makes a corresponding change to its database, the updated information is sent to the aggregator; and (4) the aggregator makes the updated information available for query by all users. Note that even if a provider takes no action regarding the suggested information, the annotations placed by the aggregator are nevertheless available to users. Additionally, because the quantifications of data quality and use described in the text allow for benchmarks that can be tracked over time, we anticipate that the feedback pendulum will help providers become more successful in justifying and securing funding to make data improvements based on feedback from users.
Supplementary material 3 from: Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM (2018) Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. ZooKeys 779: 51-88. https://doi.org/10.3897/zookeys.779.25964
Supplementary material 3 from: Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM (2018) Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. ZooKeys 779: 51-88. https://doi.org/10.3897/zookeys.779.25964
Supplementary material 1 from: Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM (2018) Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. ZooKeys 779: 51-88. https://doi.org/10.3897/zookeys.779.25964
Supplementary material 1 from: Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM (2018) Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. ZooKeys 779: 51-88. https://doi.org/10.3897/zookeys.779.25964
Supplementary material 2 from: Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM (2018) Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. ZooKeys 779: 51-88. https://doi.org/10.3897/zookeys.779.25964
Supplementary material 2 from: Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM (2018) Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. ZooKeys 779: 51-88. https://doi.org/10.3897/zookeys.779.25964
Data from: The trouble with triplets in biodiversity informatics: a data-driven case against current identifier practices
The biodiversity informatics community has discussed aspirations and approaches for assigning globally unique identifiers (GUIDs) to biocollections for nearly a decade. During that time, and despite misgivings, the de facto standard identifier has become the "Darwin Core Triplet", which is a concatenation of values for institution code, collection code, and catalog number associated with biocollections material. Our aim is not to rehash the challenging discussions regarding which GUID system in theory best supports the biodiversity informatics use case of discovering and linking digital data across the Internet, but how well we can link those data together at this moment, utilizing the current identifier schemes that have already been deployed. We gathered Darwin Core Triplets from a subset of VertNet records, along with vertebrate records from GenBank and the Barcode of Life Data System, in order to determine how Darwin Core Triplets are deployed "in the wild". We asked if those triplets follow the recommended structure and whether they provide an easy and unambiguous means to track from specimen records to genetic sequence records. We show that Darwin Core Triplets are often riddled with semantic and syntactic errors when deployed and curated in practice, despite specifications about how to construct them. Our results strongly suggest that Darwin Core Triplets that have not been carefully curated are not currently serving a useful role for relinking data. We briefly consider needed next steps to overcome current limitations.
Supplementary material 3 from: Bingham H, Doudin M, Weatherdon L, Despot-Belmonte K, Wetzel F, Groom Q, Lewis E, Regan E, Appeltans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K, Kim H, Archambeau A, Häuser C, Schmeller D, Geijzendorffer I, García Camacho A, Guerra C, Robertson T, Runnel V, Valland N, Martin C (2017) The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcomes 3: e14059. https://doi.org/10.3897/rio.3.e14059
Figures 1 -3: high resolution
Supplementary material 2 from: Bingham H, Doudin M, Weatherdon L, Despot-Belmonte K, Wetzel F, Groom Q, Lewis E, Regan E, Appeltans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K, Kim H, Archambeau A, Häuser C, Schmeller D, Geijzendorffer I, García Camacho A, Guerra C, Robertson T, Runnel V, Valland N, Martin C (2017) The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcomes 3: e14059. https://doi.org/10.3897/rio.3.e14059
MATLAB code
Supplementary material 1 from: Bingham H, Doudin M, Weatherdon L, Despot-Belmonte K, Wetzel F, Groom Q, Lewis E, Regan E, Appeltans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K, Kim H, Archambeau A, Häuser C, Schmeller D, Geijzendorffer I, García Camacho A, Guerra C, Robertson T, Runnel V, Valland N, Martin C (2017) The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcomes 3: e14059. https://doi.org/10.3897/rio.3.e14059
Biodiversity Informatics Landscape Matrix
Figure 4 from: Bingham H, Doudin M, Weatherdon L, Despot-Belmonte K, Wetzel F, Groom Q, Lewis E, Regan E, Appeltans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K, Kim H, Archambeau A, Häuser C, Schmeller D, Geijzendorffer I, García Camacho A, Guerra C, Robertson T, Runnel V, Valland N, Martin C (2017) The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcomes 3: e14059. https://doi.org/10.3897/rio.3.e14059
Figure 4 - The network of biodiversity informatics organisations. The network visualisation was created using NodeXL (Version 1.0.1.229) (Smith et al. 2009) and was laid out with the Harel–Koren Fast Multiscale algorithm and then adjusted manually to remove overlaps. The colours represent clusters identified using the Girvan–Newman algorithm.
Figure 3 from: Bingham H, Doudin M, Weatherdon L, Despot-Belmonte K, Wetzel F, Groom Q, Lewis E, Regan E, Appeltans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K, Kim H, Archambeau A, Häuser C, Schmeller D, Geijzendorffer I, García Camacho A, Guerra C, Robertson T, Runnel V, Valland N, Martin C (2017) The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcomes 3: e14059. https://doi.org/10.3897/rio.3.e14059
Figure 3 - An example of links from the biodiversity informatics landscape to the policy-level: the Biodiversity Indicators Partnership (BIP).
Figure 2 from: Bingham H, Doudin M, Weatherdon L, Despot-Belmonte K, Wetzel F, Groom Q, Lewis E, Regan E, Appeltans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K, Kim H, Archambeau A, Häuser C, Schmeller D, Geijzendorffer I, García Camacho A, Guerra C, Robertson T, Runnel V, Valland N, Martin C (2017) The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcomes 3: e14059. https://doi.org/10.3897/rio.3.e14059
Figure 2 - A highly-connected element in the landscape: the Global Biodiversity Information Facility (GBIF).
Figure 3 from: Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM (2018) Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. ZooKeys 779: 51-88. https://doi.org/10.3897/zookeys.779.25964
Figure 3 - Historical distribution of the nominate sable subspecies ( Hippotragus niger niger ), Kirk's sable ( H. niger kirkii ) and the giant sable ( H. niger variani ) in Angola based on records of the Instituto de Investigação Científica Tropical (IICT) in Portugal (obtained via GBIF search). Protected areas where H. n. niger and H. n. variani currently known to occur are indicated in the legend. The subspecies H. n. kirkii from eastern Angola has not been recorded during the past 40 years.
Figure 1 from: Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM (2018) Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. ZooKeys 779: 51-88. https://doi.org/10.3897/zookeys.779.25964
Figure 1 - Map of Angola showing spatial occurrence of mammal records obtained from various sources, including the present study which reported on captures of small mammals and acoustic recordings of the echolocation calls of bats. Although the Cuito-Okavango River trip of 2015 extended beyond Angola into Namibia and Botswana, there were no species identified from acoustic data in Namibia and Botswana that were not also detected in Angola.
Figure 2 from: Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM (2018) Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. ZooKeys 779: 51-88. https://doi.org/10.3897/zookeys.779.25964
Figure 2 - Histogram summarising species number of Angolan terrestrial mammals per order based on Hill and Carter (1943) and the current study.
Figure 4 from: Baker E, Johnson K, Young J (2011) The future of the past in the present: biodiversity informatics and geological time. ZooKeys 150: 397-405. https://doi.org/10.3897/zookeys.150.2350
Figure 4 - An example Sample record from IPAEG showing user-linked/edited age ranges (above) and calculated union and intersection dates (below).
Data from: The trouble with triplets in biodiversity informatics: a data-driven case against current identifier practices
Open the record for dataset details and reuse information.
Figure 1 from: Bingham H, Doudin M, Weatherdon L, Despot-Belmonte K, Wetzel F, Groom Q, Lewis E, Regan E, Appeltans W, Güntsch A, Mergen P, Agosti D, Penev L, Hoffmann A, Saarenmaa H, Geller G, Kim K, Kim H, Archambeau A, Häuser C, Schmeller D, Geijzendorffer I, García Camacho A, Guerra C, Robertson T, Runnel V, Valland N, Martin C (2017) The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Research Ideas and Outcomes 3: e14059. https://doi.org/10.3897/rio.3.e14059
Figure 1 - A non-exhaustive map of the global and European biodiversity informatics landscape.
Figure 5 from: Baker E, Johnson K, Young J (2011) The future of the past in the present: biodiversity informatics and geological time. ZooKeys 150: 397-405. https://doi.org/10.3897/zookeys.150.2350
Figure 5 - Calculation of the union and intersect.
Figure 3 from: Baker E, Johnson K, Young J (2011) The future of the past in the present: biodiversity informatics and geological time. ZooKeys 150: 397-405. https://doi.org/10.3897/zookeys.150.2350
Figure 3 - Data model for IPAEG
Figure 1 from: Baker E, Johnson K, Young J (2011) The future of the past in the present: biodiversity informatics and geological time. ZooKeys 150: 397-405. https://doi.org/10.3897/zookeys.150.2350
Figure 1 - Data model for Nannotax
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.