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Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science

Nico Cellinese, Reed Beaman
<span title="2012-07-20">2012</span> <i title="Pensoft Publishers"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tz6mpaaaozaoxcsg56cjcauddi" style="color: black;">ZooKeys</a> </i> &nbsp;
downstream value, for example, in the management of natural resources, policy development, food security, and planetary and human health.  ...  The acquisition and use of scientific collections is a global endeavor, and digitization enhances their value by improved access to core biodiversity information, increases use, relevance and potential  ...  Finally, we are very grateful to the National Science Foundation (DBI 0956371) for supporting our work that fostered the ideas expressed here.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3897/zookeys.209.3313">doi:10.3897/zookeys.209.3313</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22859875">pmid:22859875</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3406463/">pmcid:PMC3406463</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fvj4rhnlojd3nbzufjx2el6ig4">fatcat:fvj4rhnlojd3nbzufjx2el6ig4</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3406463/PMC3406463-zookeys.209.3313.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/ac/acaccd698a2831d1b9ecbcc15ab841e42c7da97a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3897/zookeys.209.3313"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406463" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Integrating ABCD and DarwinCore: Toward a better foundation for biodiversity information standards

Stanley Blum, Katharine Barker, Steven J Baskauf, Walter G. Berendsohn, Pier Luigi Buttigieg, Markus Döring, Gabriele Droege, David Fichtmueller, Falko Glöckler, Anton Güntsch, Robert Guralnick, Jana Hoffmann (+11 others)
<span title="2019-07-02">2019</span> <i title="Pensoft Publishers"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cvn3ubdu7vac5pnihczw5ugcsy" style="color: black;">Biodiversity Information Science and Standards</a> </i> &nbsp;
We appreciate that many working scientists and data managers perceive ontologies as overly complicated.  ...  In addition, the BioCollections Ontology (BCO) covers many of the shared concepts and is derived from the Basic Formal Ontology (BFO), an upper level ontology that has oriented many other biomedical ontologies  ...  We appreciate that many working scientists and data managers perceive ontologies as overly complicated.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3897/biss.3.37491">doi:10.3897/biss.3.37491</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lt2fkua4bvem3ajgat6htqy5uu">fatcat:lt2fkua4bvem3ajgat6htqy5uu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220117185403/https://public.pensoft.net/items/?p=7TVeXpoqfNYT89tyrm3ifrTeG9Wv8P676JSQp%2FH2pj9hhtoybol4GF7LEbj3fxHT5Fo8esHsttwAZpZjaRLDH3CmfZQoKskWV9Nw4C%2FPEAeuKic%2Bqw%3D%3D&amp;n=gBN9eeovb9Ybv8RjkCq8KeSbUMi4uQ%3D%3D" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3c/53/3c53f20ac0cdd89ead1c10427627e409ec2d0173.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3897/biss.3.37491"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Community Next Steps for Making Globally Unique Identifiers Work for Biocollections Data

Robert P. Guralnick, Nico Cellinese, John Deck, Richard L. Pyle, John Kunze, Lyubomir Penev, Ramona Walls, Gregor Hagedorn, Donat Agosti, John Wieczorek, Terry Catapano, Roderic Page
<span title="2015-04-06">2015</span> <i title="Pensoft Publishers"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tz6mpaaaozaoxcsg56cjcauddi" style="color: black;">ZooKeys</a> </i> &nbsp;
For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point  ...  on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier.  ...  We thank the Stockholm Natural History Museum for providing us with the venue and appreciate the coordination with the TDWG executive and organizing committees.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3897/zookeys.494.9352">doi:10.3897/zookeys.494.9352</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25901117">pmid:25901117</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4400380/">pmcid:PMC4400380</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7bziq3734jgkxokkacdt3n4ic4">fatcat:7bziq3734jgkxokkacdt3n4ic4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428045547/http://eprints.gla.ac.uk/105779/1/105779.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e5/95/e595c5cbc3293b296d8dd52ff0c552a19e2994ed.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3897/zookeys.494.9352"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4400380" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Herbarium data: Global biodiversity and societal botanical needs for novel research

Shelley A. James, Pamela S. Soltis, Lee Belbin, Arthur D. Chapman, Gil Nelson, Deborah L. Paul, Matthew Collins
<span title="">2018</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yrdcispkyrgjflqjazx4dqjjfe" style="color: black;">Applications in Plant Sciences</a> </i> &nbsp;
ACKNOWLEDGMENTS Integrated Digitized Biocollections (iDigBio) is funded by grants from the U.S.  ...  Integration of neontological and paleontological biodiversity data, linking with literature-based occurrence data found in resources such as the Paleobiology Database (PaleoDB; https://paleobiodb.org/)  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/aps3.1024">doi:10.1002/aps3.1024</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29732255">pmid:29732255</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5851569/">pmcid:PMC5851569</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pudo624wpncxjdje7wctu2rl2u">fatcat:pudo624wpncxjdje7wctu2rl2u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206093433/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5851569&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d9/31/d9313bc2c3ffa907976ca4ecbbf60229bf4f98a5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/aps3.1024"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5851569" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Atlas of Living Australia: History, current state and future directions

Lee Belbin, Elycia Wallis, Donald Hobern, Andre Zerger
<span title="2021-04-21">2021</span> <i title="Pensoft Publishers"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/sbmgynpwvrgmziszny3vrtfn6a" style="color: black;">Biodiversity Data Journal</a> </i> &nbsp;
It details the biodiversity and related data and services delivered to users with a primary focus on species occurrence records which represent the ALA's primary data type.  ...  The ALA has also played an important leadership role internationally in the biodiversity informatics and infrastructure space, both through its partnership with the Global Biodiversity Information Facility  ...  biodiversity data infrastructure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3897/bdj.9.e65023">doi:10.3897/bdj.9.e65023</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33935559">pmid:33935559</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8081701/">pmcid:PMC8081701</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3sw5bdq6ljdcfclx6gsgcwavaq">fatcat:3sw5bdq6ljdcfclx6gsgcwavaq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210504212219/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC8081701&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f5/01/f501393fbfdef071529d6bc64d295b58080bc997.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3897/bdj.9.e65023"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081701" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web

Brian J Stucky, John Deck, Tom Conlin, Lukasz Ziemba, Nico Cellinese, Robert Guralnick
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Recent years have brought great progress in efforts to digitize the world's biodiversity data, but integrating data from many different providers, and across research domains, remains challenging.  ...  Such slow uptake has been due, in part, to the relative complexity of Semantic Web technologies along with a lack of domain-specific software tools to help non-experts publish their data to the Semantic  ...  Heidorn, Hilmar Lapp, Richard Pyle, Tim Robertson and Robert Whitton for the constructive feedback and many discussions that took place throughout the course of software development.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-257">doi:10.1186/1471-2105-15-257</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25073721">pmid:25073721</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4124153/">pmcid:PMC4124153</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kcf4mbjomvcabgcl4qjjyp5wz4">fatcat:kcf4mbjomvcabgcl4qjjyp5wz4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829185256/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-15-257?site=http://bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/49/f5/49f5d4ede45c5549dad29998bc66839d916f52de.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-257"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124153" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Collaborative Research: ABI Development: Enabling Species Interaction Research Using Specimens and Observations (Associate!)

Katja Seltmann, Jorrit Poelen, Nico Franz, Edward Gilbert
<span title="2017-10-05">2017</span> <i title="Figshare"> Figshare </i> &nbsp;
The project summary and description for the 2017 version of the Associate! project. Associate!  ...  is a software ecosystem to facilitate research about species interactions, synthesize new data that include them, and to combine extant species interaction data resources, yielding new knowledge bases  ...  The recipes will act as repeatable usability tests for the Composer and GloBI/Symbiota extensions, and the data output for integration with other biodiversity informatics projects.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.5473135.v3">doi:10.6084/m9.figshare.5473135.v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/matxkt7tn5avtmhzc35fb5exca">fatcat:matxkt7tn5avtmhzc35fb5exca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200301210125/https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/9465757/AssociateProject.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2c/d0/2cd0cd2ef36b0a762ed16dcec9d6da265d648815.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.5473135.v3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> figshare.com </button> </a>

Meeting report: Identifying practical applications of ontologies for biodiversity informatics

John Deck, Robert Guralnick, Ramona Walls, Stanley Blum, Melissa Haendel, Andréa Matsunaga, John Wieczorek
<span title="2015-05-17">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5xcscx7glffihaolts5vo2ioaa" style="color: black;">Standards in Genomic Sciences</a> </i> &nbsp;
This report describes the outcomes of a recent workshop, building on a series of workshops from the last three years with the goal if integrating genomics and biodiversity research, with a more specific  ...  In addition, the workshop participants reviewed technical specifications and approaches for annotating instance data with BCO terms.  ...  Consortium (NSF-DBI-0840989), and by Collaborative Research: BiSciCol Tracker: Towards a tagging and tracking infrastructure for biodiversity science collections (NSF-DBI: 0956371, 0956350, 0956426.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40793-015-0014-0">doi:10.1186/s40793-015-0014-0</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iotvefylyrfq3mucgwgsvbv7ae">fatcat:iotvefylyrfq3mucgwgsvbv7ae</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813033326/https://standardsingenomics.biomedcentral.com/track/pdf/10.1186/s40793-015-0014-0?site=standardsingenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3c/3e/3c3efefc55767ab62595a07de32b3b5845e727e7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40793-015-0014-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Enabling decisions that make a difference: guidance for improving access to and analysis of invasive species information

Rebekah D. Wallace, Charles T. Bargeron, Jamie K. Reaser
<span title="2019-11-22">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/btds7yvri5cmpgrblr77mykhqe" style="color: black;">Biological Invasions</a> </i> &nbsp;
data integrators/clearinghouses; establishing an agreement for sharing data among the primary US invasive species information systems; enhancing the Integrated Taxonomic Information System to fully cover  ...  US engagement in international invasive species data sharing platforms; and continuing US membership in the Global Biodiversity Information Facility.  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10530-019-02142-2">doi:10.1007/s10530-019-02142-2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/orvmum3klvakzenuwvrl3mrxyy">fatcat:orvmum3klvakzenuwvrl3mrxyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200325093309/https://link.springer.com/content/pdf/10.1007/s10530-019-02142-2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9c/02/9c0265b0676966adde37e5707d06261256451b09.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10530-019-02142-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Towards global data products of Essential Biodiversity Variables on species traits

W. Daniel Kissling, Ramona Walls, Anne Bowser, Matthew O. Jones, Jens Kattge, Donat Agosti, Josep Amengual, Alberto Basset, Peter M. van Bodegom, Johannes H. C. Cornelissen, Ellen G. Denny, Salud Deudero (+17 others)
<span title="2018-09-17">2018</span> <i title="Springer Nature America, Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pe7lkozg4vfr5emegexceqa4ia" style="color: black;">Nature Ecology &amp; Evolution</a> </i> &nbsp;
We evaluate the societal relevance of species traits EBVs for policy targets and demonstrate how open, interoperable and machine-readable trait data enable the building of EBV data products.  ...  Essential Biodiversity Variables (EBVs) allow observation and reporting of global biodiversity change, but a detailed framework for the empirical derivation of specific EBVs has yet to be developed.  ...  biocollections with specimen-related trait data from museums and herbaria (for example, VertNet) Examples of trait databases Monitoring networks with focus on species traits (for example, NEON  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41559-018-0667-3">doi:10.1038/s41559-018-0667-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30224814">pmid:30224814</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ocmffeznebanfenwy33nuhakre">fatcat:ocmffeznebanfenwy33nuhakre</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430122316/http://plymsea.ac.uk/id/eprint/8068/1/s41559-018-0667-3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5d/ed/5dedd0ec12e09640dea10f88ad6b8cf6cdc7d90d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41559-018-0667-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

Decentralized but Globally Coordinated Biodiversity Data

Beckett W. Sterner, Edward E. Gilbert, Nico M. Franz
<span title="2020-10-23">2020</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zsdtezgyevhsxncisld4z5oxfe" style="color: black;">Frontiers in Big Data</a> </i> &nbsp;
With no single aggregator to exert centralized control over biodiversity data, decentralization generates loosely connected networks of mid-level aggregators.  ...  The decentralized model also poses novel integration challenges, among which the explicit and continuous articulation of conflicting systematic classifications and phylogenies remain the most challenging  ...  ACKNOWLEDGMENTS We would like to acknowledge several funding sources that have supported this work along with discussions with David Remsen, Anne Thessen, Katja Seltmann, Atriya Sen, and Steve Elliott.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fdata.2020.519133">doi:10.3389/fdata.2020.519133</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33693407">pmid:33693407</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7931950/">pmcid:PMC7931950</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2w4ouywvkvgovbfpaykhsjutju">fatcat:2w4ouywvkvgovbfpaykhsjutju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201027144056/https://fjfsdata01prod.blob.core.windows.net/articles/files/519133/pubmed-zip/.versions/2/.package-entries/fdata-03-519133-r1/fdata-03-519133.pdf?sv=2018-03-28&amp;sr=b&amp;sig=Gt0lT1nd01%2B4lP1onFAotEZMZ3PKfv159SMkVCKzv1E%3D&amp;se=2020-10-27T14%3A41%3A25Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fdata-03-519133.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2e/9c/2e9c7e34ed17d8113631722fb3689bee1701d2b4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fdata.2020.519133"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931950" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The importance of digitized biocollections as a source of trait data and a new VertNet resource

Robert P. Guralnick, Paula F. Zermoglio, John Wieczorek, Raphael LaFrance, David Bloom, Laura Russell
<span title="">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
The importance of digitized biocollections as a source of trait data and a new VertNet resource.  ...  in VertNet, a global biodiversity data publisher and aggregator.  ...  We thank to all those in the collections, macroevolutionary, and macroecology communities whose perspective helped us to determine if this effort might be fruitful, especially Ethan White, Morgan Ernst  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw158">doi:10.1093/database/baw158</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28025346">pmid:28025346</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5199146/">pmcid:PMC5199146</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fxrqngh7ivcwtic7ehjidsyjta">fatcat:fxrqngh7ivcwtic7ehjidsyjta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218154409/http://pdfs.semanticscholar.org/0daf/5bb22792e4042f18aebcf76430ce854301b6.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0d/af/0daf5bb22792e4042f18aebcf76430ce854301b6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw158"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199146" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

John Wieczorek, David Bloom, Robert Guralnick, Stan Blum, Markus Döring, Renato Giovanni, Tim Robertson, David Vieglais, Indra Neil Sarkar
<span title="2012-01-06">2012</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information.  ...  Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms.  ...  with mapping Darwin Core and ABCD crosswalking, Dag Endresen for due dilligence with germplasm extension, and Gail Kampmeier who steered the review of Darwin Core on a straight course when it was up for  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0029715">doi:10.1371/journal.pone.0029715</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22238640">pmid:22238640</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3253084/">pmcid:PMC3253084</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q37kzb7dibewjn7olp5nu5zir4">fatcat:q37kzb7dibewjn7olp5nu5zir4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190505213255/https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0029715&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/54/4a/544aff5a6bcb7f838c3b598eaf979100db3557c3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0029715"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3253084" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Sample Identifiers and Metadata to Support Data Management and Reuse in Multidisciplinary Ecosystem Sciences

Joan E. Damerow, Charuleka Varadharajan, Kristin Boye, Eoin L. Brodie, Madison Burrus, K. Dana Chadwick, Robert Crystal-Ornelas, Hesham Elbashandy, Ricardo J. Eloy Alves, Kim S. Ely, Amy E. Goldman, Ted Haberman (+14 others)
<span title="2021-03-18">2021</span> <i title="Ubiquity Press, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6c6hoxo2t5fhvmt3alezyxsomy" style="color: black;">Data Science Journal</a> </i> &nbsp;
Data generated from sample-based analyses are not only the basis of individual studies, but can also be integrated with other data to answer new and broader-scale questions.  ...  Our goal is to provide a practical approach to sample management, geared towards ecosystem scientists who contribute and reuse sample data.  ...  We also thank Jens Klump for guidance on related work, Chris Mungall for guidance on ontology use and ENVO.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5334/dsj-2021-011">doi:10.5334/dsj-2021-011</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p4wpadnnq5g7hbylv3bkzrwoka">fatcat:p4wpadnnq5g7hbylv3bkzrwoka</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210319134727/https://datascience.codata.org/articles/10.5334/dsj-2021-011/galley/1055/download/" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/96/fc/96fc039f6ce7e62dd4f10e4ad16ead78468b842e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5334/dsj-2021-011"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Integrating herbarium specimen observations into global phenology data systems

Laura Brenskelle, Brian J. Stucky, John Deck, Ramona Walls, Rob P. Guralnick
<span title="2019-03-07">2019</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yrdcispkyrgjflqjazx4dqjjfe" style="color: black;">Applications in Plant Sciences</a> </i> &nbsp;
With the incorporation of herbarium phenology data, new historical baseline data will strengthen the capability to monitor, model, and forecast plant phenology changes.  ...  Here we describe a new release of the PPO and associated data pipelines that supports integration of phenology observations from herbarium specimens, which provide historical and modern phenology data.  ...  ., and R.W. made needed changes to the Plant Phenology Ontology and dealt with managing new releases.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/aps3.1231">doi:10.1002/aps3.1231</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30937223">pmid:30937223</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6426164/">pmcid:PMC6426164</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6omgvriatje6rgr3itthoxik6e">fatcat:6omgvriatje6rgr3itthoxik6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191209020556/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6426164&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/78/7b/787b9121c569e76b4773120b34a4736d7d4a0b0e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/aps3.1231"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426164" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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