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Community next steps for making globally unique identifiers work for biocollections data.

Guralnick RP, Cellinese N, Deck J, Pyle RL, Kunze J, Penev L, Walls R, Hagedorn G, Agosti D, Wieczorek J, Catapano T, Page RD - Zookeys (2015)

Bottom Line: Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets.There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses.Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.

View Article: PubMed Central - HTML - PubMed

Affiliation: Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-2710 USA.

ABSTRACT
Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. 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 when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.

No MeSH data available.


Related in: MedlinePlus

Example of a PURL-URI as a QR-Code, in this example attached to a digitised lichen type specimen in the Natural History Museum, University of Oslo. The QR-Code corresponds to http://purl.org/nhmuio/id/c1a8b878-a4f9-448b-be00-26cbad58b11c.
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Figure 2: Example of a PURL-URI as a QR-Code, in this example attached to a digitised lichen type specimen in the Natural History Museum, University of Oslo. The QR-Code corresponds to http://purl.org/nhmuio/id/c1a8b878-a4f9-448b-be00-26cbad58b11c.

Mentions: For newly collected samples, a highly desirable next step is the ability to assign globally unique identifiers directly to newly collected specimens or mixed samples in the field or shortly thereafter. In many cases, it may be desirable that these identifiers be pre-minted and written into a physical barcode or QR-Code, perhaps in conjunction with a human-friendly identifier. Figures 1 and 2 show different examples, the first representing a traditional biocollections object and the second depicting mass-labeling of tubes associated with collections samples. Assigning GUIDs to specimens at the time of collection allows field researchers to publish references to recently collected specimens without waiting for institutional identifiers that are assigned during the accession process. Beyond simply assigning unique identifiers in the field, it is critical that these identifiers persist perpetually with the objects they identify and all descendant samples, subsamples, analyses, data and publications referring to them, ensuring an unbroken chain of data provenance. In the best of all possible worlds, identifiers assigned in the field are retained as the permanent institutional identifier during accessioning.


Community next steps for making globally unique identifiers work for biocollections data.

Guralnick RP, Cellinese N, Deck J, Pyle RL, Kunze J, Penev L, Walls R, Hagedorn G, Agosti D, Wieczorek J, Catapano T, Page RD - Zookeys (2015)

Example of a PURL-URI as a QR-Code, in this example attached to a digitised lichen type specimen in the Natural History Museum, University of Oslo. The QR-Code corresponds to http://purl.org/nhmuio/id/c1a8b878-a4f9-448b-be00-26cbad58b11c.
© Copyright Policy - creative-commons-attribution
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4400380&req=5

Figure 2: Example of a PURL-URI as a QR-Code, in this example attached to a digitised lichen type specimen in the Natural History Museum, University of Oslo. The QR-Code corresponds to http://purl.org/nhmuio/id/c1a8b878-a4f9-448b-be00-26cbad58b11c.
Mentions: For newly collected samples, a highly desirable next step is the ability to assign globally unique identifiers directly to newly collected specimens or mixed samples in the field or shortly thereafter. In many cases, it may be desirable that these identifiers be pre-minted and written into a physical barcode or QR-Code, perhaps in conjunction with a human-friendly identifier. Figures 1 and 2 show different examples, the first representing a traditional biocollections object and the second depicting mass-labeling of tubes associated with collections samples. Assigning GUIDs to specimens at the time of collection allows field researchers to publish references to recently collected specimens without waiting for institutional identifiers that are assigned during the accession process. Beyond simply assigning unique identifiers in the field, it is critical that these identifiers persist perpetually with the objects they identify and all descendant samples, subsamples, analyses, data and publications referring to them, ensuring an unbroken chain of data provenance. In the best of all possible worlds, identifiers assigned in the field are retained as the permanent institutional identifier during accessioning.

Bottom Line: Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets.There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses.Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.

View Article: PubMed Central - HTML - PubMed

Affiliation: Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-2710 USA.

ABSTRACT
Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. 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 when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.

No MeSH data available.


Related in: MedlinePlus