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Fig. 3 in Re-description of two marine sponge species (Demospongiae: Haplosclerida) from the coast of Karachi, Pakistan, Northern Arabian Sea
Fig. 3 — (a) Specimen of Callyspongia (Cladochalina) fibrosa (Ridley and Dendy, 1886), (b) Light microscopic image of tangential skeleton shows tufted spongin network (scale = 20 µm), (c) Light microscopic image of microtome-section showing spiculo-fibres, and (d) Scanning electron microscopic image of siliceous spicules (scale = 5 µm)
Fig. 1 in Re-description of two marine sponge species (Demospongiae: Haplosclerida) from the coast of Karachi, Pakistan, Northern Arabian Sea
Fig. 1 — Map of Karachi, Pakistan coast showing the collection site of Churna Island and Buleji. (Google Earth Pro: version 7.1.4.1529)
Figure 1 in Developing biosecurity plans for non-native species in marine dependent areas: the role of legislation, risk management and stakeholder engagement
Figure 1. Five-stage approach for risk assessment management of NNS in Shetland, adapted from the ecosystem-based risk management framework (Cormier et al. 2013).
Figure 4 in The marine live bait trade as a pathway for the introduction of non-indigenous species into California: patterns of importation and thermal tolerances of imported specimens
Figure 4. Average percent survival (± SE) of G. dibranchiata (A) and Perinereis sp. (B) after exposed to southern California thermal conditions for five days. Gray bars indicate significant difference. No difference in survival was observed among the three temperature treatments for G. dibranchiata (F2,8 = 2.67, p = 0.130). There was a significant difference in survival of Perinereis sp. among the treatments (F2,8 = 11.08, p = 0.005).
Figure 1 in The marine live bait trade as a pathway for the introduction of non-indigenous species into California: patterns of importation and thermal tolerances of imported specimens
Figure 1. Distribution by county of bait shops selling marine live bait in California according to survey responses. Live marine bait was sold in all counties shaded in grey. Numbers inside black circles indicate species sold in that county. Bait shops in shaded counties without black circles reported marine live bait sales but did not provide information on which species they sold.
Figure 3 in The marine live bait trade as a pathway for the introduction of non-indigenous species into California: patterns of importation and thermal tolerances of imported specimens
Figure 3. For each species of marine live bait, (A) the percentage of respondents who reported importing that species who answered that either seaweed (sometimes in combination with newspaper) or seawater were used as packing materials, and (B) the percentage of respondents who reported importing that species who observed hitchhikers in shipments of that species. Note that for (A), some respondents indicated that both seaweed and seawater were used as packing materials for a given species, so that the total percentage may add up to greater than 100 (e.g., for pileworms).
Figure 1 in A low number of introduced marine species in the tropics: a case study from Singapore
Figure 1. Map of Singapore showing localities mentioned in the text and the amount of land reclaimed since 1950.
World Register of Marine Species (WoRMS) Repackaged hash://sha256/4e969a1c8243b523b093d3a05fd5f7683479c2919e7d83e8b1383c5e5ef1d4e5 hash://md5/fb7559ce707d11f96a878d8a8a79a661
<h1>Introduction</h1> <p>The World Register of Marine Species (WoRMS) (Ahyong et al. 2024) aims to “[…] provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. While the highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature. […]”</p> <p>This data publication contains a verifiable copy of the World Register of Marine Species as well as a streamable version in json-line format. The aims of this publication are to:</p> <ol> <li> <p>provide a signed citation (Elliott, Poelen, and Fortes 2023) for a copy of WoRMS</p> </li> <li> <p>prepare WoRMS to be included in the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2023).</p> </li> <li> <p>pre-process the World Register of Marine Species to facilitate optimized indexing and offline taxonomic name alignments using tools like Nomer (J. Poelen and Salim 2023).</p> </li> </ol> <p>Overall, the publications aims to facilitate taxonomic name alignment using the wealth of information provided by the World Register of Marine Species (WoRMS) to help enable fast, reproduceable, offline-enabled alignment of namelists with taxonomic resources of known provenance (or origin).</p> <p>An example of an application facilitated by this publication is the Taxonomic Name Alignment tool as provided through https://github.com/globalbioticinteractions/name-alignment-template. This template repository implements an automated workflow using GitHub Action to align scientific names in csv/tsv files and darwin core archive with common taxonomic name lists like WoRMS, NCBI Taxonomy, Integrated Taxonomic Information System (ITIS), and GBIF Backbone taxonomy.</p> <h2><a name="methods"></a>Methods</h2> <p>To capture and process WoRMS, the following steps were taken:</p> <ol> <li> <p>re-use a tracked and archived copy of WoRMS</p> </li> <li> <p>make WoRMS archive streamable by translating the WoRMS DwC-A into a line-json</p> </li> <li> <p>assign an alias to the processed resources</p> </li> </ol> <p>Steps 1-3 are captured and documented using Preston, a biodiversity data tracker. Preston not only helps to documents the steps, but also includes the digital resources that were used and produced.</p> <h3><a name="reuse-versioned-worms-archive"></a>Reuse Versioned WoRMS Archive</h3> <p>To reuse a versioned copy of June 2024 WoRMS as provided through Checklist Bank, the following command was issued:</p> <pre># define dependency on a June 2024 version of Checklist Bank. preston use hash://sha256/763edde4043c32ff53b9d8fc945a67b6409adccc0757a3bff1e52cccd4802476 # resolve WoRMS by their Checklist Bank Alias preston cat hash://sha256/763edde4043c32ff53b9d8fc945a67b6409adccc0757a3bff1e52cccd4802476\ --remote https://linker.bio\ | grep hasVersion\ | grep "https://api.checklistbank.org/dataset/2011/archive.zip"\ | head -1\ | preston dwc-stream --remote https://linker.bio\ | gzip\ | preston track # define an alias short cut to the generated json.gz archive preston head\ | preston cat\ | grep hasVersion\ | grep -oE "hash://[a-z0-9]+/[a-f0-9]+"\ | xargs -L1 preston alias worms:worms.json.gz</pre> <p>With this, a previously archived copy of https://api.checklistbank.org/dataset/2011/archive.zip is downloaded and their sha256 checksum (or hash) is calculated. Also, the download process was previously captured machine-readable rdf/nquads statement of hash://sha256/763edde4043c32ff53b9d8fc945a67b6409adccc0757a3bff1e52cccd4802476.</p> <p>An example record from the derived dataset worms:worms.json.gz included in this publication can be found using:</p> <pre>preston alias\ --anchor hash://sha256/4e969a1c8243b523b093d3a05fd5f7683479c2919e7d83e8b1383c5e5ef1d4e5\ --remote https://zenodo.org/deposit/8327611/files\ worms:worms.json.gz\ | preston cat\ | gunzip\ | head -n1\ | jq .</pre> <p>and is</p> <pre>{ "http://www.w3.org/ns/prov#wasDerivedFrom": "line:zip:hash://sha256/ca4baa1a90f4ce80d27ec7d1525f54a75fa679d76a66ed6143b17031287dea09!/taxon.txt!/L2", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "http://rs.tdwg.org/dwc/terms/Taxon", "http://rs.tdwg.org/dwc/text/id": "urn:lsid:marinespecies.org:taxname:1", "http://rs.tdwg.org/dwc/terms/scientificNameAuthorship": null, "http://rs.tdwg.org/dwc/terms/nomenclaturalStatus": null, "http://rs.tdwg.org/dwc/terms/acceptedNameUsage": "Biota", "http://rs.tdwg.org/dwc/terms/infraspecificEpithet": null, "http://rs.tdwg.org/dwc/terms/taxonRank": null, "http://rs.tdwg.org/dwc/terms/phylum": null, "http://rs.tdwg.org/dwc/terms/scientificNameID": "urn:lsid:marinespecies.org:taxname:1", "http://rs.tdwg.org/dwc/terms/scientificName": "Biota", "http://rs.tdwg.org/dwc/terms/parentNameUsage": "Biota", "http://rs.tdwg.org/dwc/terms/datasetName": "World Register of Marine Species (WoRMS)", "http://purl.org/dc/terms/references": "https://www.marinespecies.org/aphia.php?p=taxdetails&id=1", "http://rs.tdwg.org/dwc/terms/subgenus": null, "http://purl.org/dc/terms/rightsHolder": "WoRMS Editorial Board", "http://rs.tdwg.org/dwc/terms/family": null, "http://rs.tdwg.org/dwc/terms/order": null, "http://rs.tdwg.org/dwc/terms/class": null, "http://purl.org/dc/terms/bibliographicCitation": "WoRMS (2024). Biota. Accessed at: https://www.marinespecies.org/aphia.php?p=taxdetails&id=1", "http://rs.tdwg.org/dwc/terms/genus": null, "http://purl.org/dc/terms/license": "http://creativecommons.org/licenses/by/4.0/", "http://rs.tdwg.org/dwc/terms/namePublishedInYear": null, "http://rs.tdwg.org/dwc/terms/institutionCode": "VLIZ", "http://rs.tdwg.org/dwc/terms/acceptedNameUsageID": "urn:lsid:marinespecies.org:taxname:1", "http://rs.tdwg.org/dwc/terms/kingdom": null, "http://rs.tdwg.org/dwc/terms/taxonID": "urn:lsid:marinespecies.org:taxname:1", "http://rs.tdwg.org/dwc/terms/parentNameUsageID": null, "http://rs.tdwg.org/dwc/terms/datasetID": "https://doi.org/10.14284/170", "http://rs.tdwg.org/dwc/terms/nomenclaturalCode": null, "http://rs.tdwg.org/dwc/terms/namePublishedInID": null, "http://purl.org/dc/terms/modified": "2004-12-21", "http://rs.tdwg.org/dwc/terms/taxonomicStatus": "accepted", "http://rs.tdwg.org/dwc/terms/namePublishedIn": null, "http://rs.tdwg.org/dwc/terms/specificEpithet": null }</pre> <p>which shows the first json-line object retrieved from the WoRMS DwC-A.</p> <h1><a name="results"></a>Results</h1> <p>As described in our methods, this publication derived the resource with alias worms:worms.json.gz and content id hash://sha256/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7 . This resource contains a streamable line-json archive derived from a versioned copy package retrieved from https://api.checklistbank.org/dataset/2011/archive.zip with content identifier hash://sha256/ca4baa1a90f4ce80d27ec7d1525f54a75fa679d76a66ed6143b17031287dea09.</p> <p>The following tools were used to process the WoRMS resource:</p> <p>Tools used in this data publication</p> <table> <tbody> <tr> <th> <p>tool name</p> </th> </tr> </tbody> <tbody> <tr> <td> <p><a href="https://github.com/bio-guoda/preston">preston</a></p> </td> </tr> <tr> <td> <p><a href="https://en.wikipedia.org/wiki/Bash_(Unix_shell)">bash</a></p> </td> </tr> <tr> <td> <p><a href="https://en.wikipedia.org/wiki/Gzip">gzip</a></p> </td> </tr> <tr> <td> <p><a href="https://en.wikipedia.org/wiki/Sed">sed</a></p> </td> </tr> <tr> <td> <p><a href="https://en.wikipedia.org/wiki/Head_(Unix)">head</a></p> </td> </tr> </tbody> </table> <h1><a name="discussion"></a>Discussion</h1> <p>This publication is intended to facilitate re-use of the WoRMS data package in taxonomic name alignment workflows. While the primary goal was to generate a resource for use in Nomer v0.4.9 (J. Poelen and Salim 2023), other usage can be imagined such as:</p> <ol> <li> <p>Lots of Copies Keeps Stuff Safe (LOCKSS (Maniatis et al. 2005)): keep an identical copy of WoRMS data package outside of the Checklist Bank/ WoRMS infrastructure.</p> </li> <li> <p>making a json-line streamable copy of WoRMS available via https://zenodo.org/record/12112610/files/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7 for use in workflows like looking up the first record that contain <em>Enhydra lutris</em> (Sea otter):</p> </li> </ol> <pre> curl -L 'https://zenodo.org/record/12112610/files/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7'\ | gunzip\ | grep "Enhydra lutris"\ | head -n1\ | jq .</pre> <p>producing</p> <pre>{ "http://www.w3.org/ns/prov#wasDerivedFrom": "line:zip:hash://sha256/ca4baa1a90f4ce80d27ec7d1525f54a75fa679d76a66ed6143b17031287dea09!/taxon.txt!/L111764", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "http://rs.tdwg.org/dwc/terms/Taxon", "http://rs.tdwg.org/dwc/text/id": "urn:lsid:marinespecies.org:taxname:242598", "http://rs.tdwg.org/dwc/terms/scientificNameAuthorship": "(Linnaeus, 1758)", "http://rs.tdwg.org/dwc/terms/nomenclaturalStatus": null, "http://rs.tdwg.org/dwc/terms/acceptedNameUsage": "Enhydra lutris", "http://rs.tdwg.org/dwc/terms/infraspecificEpithet": null, "http://rs.tdwg.org/dwc/terms/taxonRank": "Species", "http://rs.tdwg.org/dwc/terms/phylum": "Chordata", "http://rs.tdwg.org/dwc/terms/scientificNameID": "urn:lsid:marinespecies.org:taxname:242598", "http://rs.tdwg.org/dwc/terms/scientificName": "Enhydra lutris", "http://rs.tdwg.org/dwc/terms/parentNameUsage": "Enhydra", "http://rs.tdwg.org/dwc/terms/datasetName": "World Register of Marine Species (WoRMS)", "http://purl.org/dc/terms/references": "https://www.marinespecies.org/aphia.php?p=taxdetails&id=242598", "http://rs.tdwg.org/dwc/terms/subgenus": null, "http://purl.org/dc/terms/rightsHolder": "WoRMS Editorial Board", "http://rs.tdwg.org/dwc/terms/family": "Mustelidae", "http://rs.tdwg.org/dwc/terms/order": "Carnivora", "http://rs.tdwg.org/dwc/terms/class": "Mammalia", "http://purl.org/dc/terms/bibliographicCitation": "WoRMS (2024). Enhydra lutris (Linnaeus, 1758). Accessed at: https://www.marinespecies.org/aphia.php?p=taxdetails&id=242598", "http://rs.tdwg.org/dwc/terms/genus": "Enhydra", "http://purl.org/dc/terms/license": "http://creativecommons.org/licenses/by/4.0/", "http://rs.tdwg.org/dwc/terms/namePublishedInYear": null, "http://rs.tdwg.org/dwc/terms/institutionCode": "VLIZ", "http://rs.tdwg.org/dwc/terms/acceptedNameUsageID": "urn:lsid:marinespecies.org:taxname:242598", "http://rs.tdwg.org/dwc/terms/kingdom": "Animalia", "http://rs.tdwg.org/dwc/terms/taxonID": "urn:lsid:marinespecies.org:taxname:242598", "http://rs.tdwg.org/dwc/terms/parentNameUsageID": "urn:lsid:marinespecies.org:taxname:242597", "http://rs.tdwg.org/dwc/terms/datasetID": "https://doi.org/10.14284/170", "http://rs.tdwg.org/dwc/terms/nomenclaturalCode": "ICZN", "http://rs.tdwg.org/dwc/terms/namePublishedInID": null, "http://purl.org/dc/terms/modified": "2010-05-20", "http://rs.tdwg.org/dwc/terms/taxonomicStatus": "accepted", "http://rs.tdwg.org/dwc/terms/namePublishedIn": null, "http://rs.tdwg.org/dwc/terms/specificEpithet": "lutris" } ``` Note that the following command should also produce the *exact* same results: </pre> <p>preston cat –remote https://linker.bio,https://zenodo.org/record/12112610/files/<br>hash://sha256/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7<br>| gunzip<br>| grep “Enhydra lutris”<br>| head -n1<br>| jq . ~~~</p> <p>and</p> <pre>preston cat --remote https://linker.bio,https://zenodo.org\ hash://sha256/0a6625167b6943d31cfa737dd5f6f123c767d236194f6a1c97c44f678d9fcaa7\ | gunzip\ | grep "Enhydra lutris"\ | head -n1\ | jq .</pre> <p>and</p> <pre>preston cat --remote https://linker.bio,https://zenodo.org\ hash://md5/aa54d0c3587526e3da167cf93afa541f\ | gunzip\ | grep "Enhydra lutris"\ | head -n1\ | jq .</pre> <h1><a name="acknowledgements"></a>Acknowledgements</h1> <p>This work stands on the shoulders of contributors to open source software and openly accessible datasets. Thank you!</p> <h1><a name="bibliography"></a>References</h1> <div> <p>Ahyong, S., C. B. Boyko, N. Bailly, J. Bernot, R. Bieler, S. N. Brandão, M. Daly, et al. 2024. “World Register of Marine Species (WoRMS).” WoRMS Editorial Board. <a href="https://www.marinespecies.org/">https://www.marinespecies.org</a>. https://doi.org/10.14284/170</p> <p> </p> </div> <div> <p>Elliott, Michael J., Jorrit H. Poelen, and José A. B. Fortes. 2023. “Signing Data Citations Enables Data Verification and Citation Persistence.” <em>Scientific Data</em> 10 (1). <a href="https://doi.org/10.1038/s41597-023-02230-y">https://doi.org/10.1038/s41597-023-02230-y</a>.</p> </div> <div> <p> </p> <p>Maniatis, Petros, Mema Roussopoulos, Thomas J Giuli, David SH Rosenthal, and Mary Baker. 2005. “The LOCKSS Peer-to-Peer Digital Preservation System.” <em>ACM Transactions on Computer Systems (TOCS)</em> 23 (1): 2–50.</p> </div> <div> <p> </p> <p>Poelen, Jorrit H. (ed.). 2023. “Nomer Corpus of Taxonomic Resources hash://sha256 /12051b8aa59930d6561a3ed46b7cf3f67a31a98445a457d78 894f6b8a8e81641 hash://md5/1ff6b3628d7afc15b882cc0c9b1c3815.” Zenodo. <a href="https://doi.org/10.5281/zenodo.8326175">https://doi.org/10.5281/zenodo.8326175</a>.</p> </div> <p> </p> <p>Poelen, Jorrit, and José Augusto Salim. 2023. “Globalbioticinteractions/Nomer: 0.5.4.” Zenodo. <a href="https://doi.org/10.5281/zenodo.8329422">https://doi.org/10.5281/zenodo.8329422</a>.</p>
Figure 31 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 31. Moruloidea perionasus sp. nov. A–D, holotype, remainder male paratype, NMV J26202. A, dorsal view; B, lateral view; C, frons, ventral view; D, pleon, posterior margin, posterior view; E, antennule; F, antenna; G, maxilliped; H, penes.
Figure 40 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 40. Pedinura mokari sp. nov. A–D, holotype, remainder male paratype NMV J39721. A, dorsal view; B, lateral view; C, frons, ventral view; D, pleon and pleotelson, ventral view; E, antennule; F, antenna; G, maxilliped; H, left mandible; I, maxilla; J, maxillule.
Figure 37 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 37. Pedinura flindersia sp. nov. All figs male paratype NMV J39721. A–E, pleopods 1–5; F, uropod; G, penes.
Figure 28 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 28. Margueritta sandyi sp. nov. A–D, holotype, remainder _ paratype. A, dorsal view; B, lateral view; C, frons, ventral view; D, pleon, posterior margin, ventral view; E, antennule; F, antenna; G, maxilliped; H, right mandible.
Figure 27 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 27. Koremosphaera colonus sp. nov. Female. A. lateral view; B, pleon and pleotelson, dorsal view.
Figure 24 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 24. Koremosphaera colonus sp. nov. A, maxilliped; B, maxillule; C, maxilla; D, maxilliped endite, distal margin; E, maxillule, lateral lobe, f, gnathal RS; F, maxillule, mesial lobe; G, left mandible; H, right mandible, incisor and spine row; I, mandible palp.
Figure 34 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 34. Moruloidea perionasus sp. nov. Male paratype, NMV J26202. A–E, pleopods 1–5; F, uropod; G, detail of uropod dorsal surface.
Figure 23 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 23. Koremosphaera colonus sp. nov. A–D, holotype, remainder as indicated. A, dorsal view; B, lateral view; C, pleon, posterior margin, ventral view; D, epistome, anterior view; E, epistome, ventral view; F, antennule; G, antenna.
Figure 20 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 20. Exosphaeroma alveola sp. nov. A, maxilliped; B, maxilla; C, pereopod 1; D, pereopod 1, dactylus; E, pereopod 2; F, pereopod 7, f, RS from carpus superior distal angle.
Figure 19 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 19. Exosphaeroma alveola sp. nov. A, antennule; B, antenna; C, left mandible; D, left mandible, distal part; E, right mandible, distal part; F, mandible palp; G, maxillule; H. maxillule, gnathal end, lateral lobe; I, maxillule, lateral lobe; J, penial processes.
Figure 18 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 18. Exosphaeroma alveola sp. nov. A, B, E, G, holotype, remainder as indicated. A, dorsal view; B, lateral view; C, lateral view female; D, dorsal view, head and pereonite 1, female; E, frons; F, pleon and pleotelson, female; G, pleon, posterior margin, ventral view.
Figure 36 in New genera and species of sphaeromatid isopod crustaceans from Australian marine coastal waters
Figure 36. Pedinura flindersia sp. nov. All figs male paratype NMV J39721. A, maxilla; B, maxillule; C, pereopod 1; D, pereopod 1, dactylus; E, pereopod 2; F, pereopod 2, dactylus; G, pereopod 3; H, pereopod 6; I, pereopod 4; J, pereopod 7.
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.