The importance of digitized biocollections as a source of trait data and a new VertNet resource
For vast areas of the globe and large parts of the tree of life, data needed to inform trait diversity is incomplete. Such trait data, when fully assembled, however, form the link between the evolutionary history of organisms, their assembly into communities, and the nature and functioning of ecosys...
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17580463_v2016_n_p_Guralnick http://hdl.handle.net/20.500.12110/paper_17580463_v2016_n_p_Guralnick |
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paper:paper_17580463_v2016_n_p_Guralnick2023-06-08T16:28:58Z The importance of digitized biocollections as a source of trait data and a new VertNet resource Zermoglio, Paula Florencia animal DNA sequence genetic database genetic variation human procedures quantitative trait locus software Animals Databases, Genetic Genetic Variation Humans Quantitative Trait Loci Sequence Analysis, DNA Software For vast areas of the globe and large parts of the tree of life, data needed to inform trait diversity is incomplete. Such trait data, when fully assembled, however, form the link between the evolutionary history of organisms, their assembly into communities, and the nature and functioning of ecosystems. Recent efforts to close data gaps have focused on collating trait-by-species databases, which only provide species-level, aggregated value ranges for traits of interest and often lack the direct observations on which those ranges are based. Perhaps under-appreciated is that digitized biocollection records collectively contain a vast trove of trait data measured directly from individuals, but this content remains hidden and highly heterogeneous, impeding discoverability and use. We developed and deployed a suite of openly accessible software tools in order to collate a full set of trait descriptions and extract two key traits, body length and mass, from >18 million specimen records in VertNet, a global biodiversity data publisher and aggregator. We tested success rate of these tools against hand-checked validation data sets and characterized quality and quantity. A post-processing toolkit was developed to standardize and harmonize data sets, and to integrate this improved content into VertNet for broadest reuse. The result of this work was to add more than 1.5 million harmonized measurements on vertebrate body mass and length directly to specimen records. Rates of false positives and negatives for extracted data were extremely low. We also created new tools for filtering, querying, and assembling this research-ready vertebrate trait content for view and download. Our work has yielded a novel database and platform for harmonized trait content that will grow as tools introduced here become part of publication workflows. We close by noting how this effort extends to new communities already developing similar digitized content. © The Author(s) 2016. Fil:Zermoglio, P.F. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2016 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17580463_v2016_n_p_Guralnick http://hdl.handle.net/20.500.12110/paper_17580463_v2016_n_p_Guralnick |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
animal DNA sequence genetic database genetic variation human procedures quantitative trait locus software Animals Databases, Genetic Genetic Variation Humans Quantitative Trait Loci Sequence Analysis, DNA Software |
| spellingShingle |
animal DNA sequence genetic database genetic variation human procedures quantitative trait locus software Animals Databases, Genetic Genetic Variation Humans Quantitative Trait Loci Sequence Analysis, DNA Software Zermoglio, Paula Florencia The importance of digitized biocollections as a source of trait data and a new VertNet resource |
| topic_facet |
animal DNA sequence genetic database genetic variation human procedures quantitative trait locus software Animals Databases, Genetic Genetic Variation Humans Quantitative Trait Loci Sequence Analysis, DNA Software |
| description |
For vast areas of the globe and large parts of the tree of life, data needed to inform trait diversity is incomplete. Such trait data, when fully assembled, however, form the link between the evolutionary history of organisms, their assembly into communities, and the nature and functioning of ecosystems. Recent efforts to close data gaps have focused on collating trait-by-species databases, which only provide species-level, aggregated value ranges for traits of interest and often lack the direct observations on which those ranges are based. Perhaps under-appreciated is that digitized biocollection records collectively contain a vast trove of trait data measured directly from individuals, but this content remains hidden and highly heterogeneous, impeding discoverability and use. We developed and deployed a suite of openly accessible software tools in order to collate a full set of trait descriptions and extract two key traits, body length and mass, from >18 million specimen records in VertNet, a global biodiversity data publisher and aggregator. We tested success rate of these tools against hand-checked validation data sets and characterized quality and quantity. A post-processing toolkit was developed to standardize and harmonize data sets, and to integrate this improved content into VertNet for broadest reuse. The result of this work was to add more than 1.5 million harmonized measurements on vertebrate body mass and length directly to specimen records. Rates of false positives and negatives for extracted data were extremely low. We also created new tools for filtering, querying, and assembling this research-ready vertebrate trait content for view and download. Our work has yielded a novel database and platform for harmonized trait content that will grow as tools introduced here become part of publication workflows. We close by noting how this effort extends to new communities already developing similar digitized content. © The Author(s) 2016. |
| author |
Zermoglio, Paula Florencia |
| author_facet |
Zermoglio, Paula Florencia |
| author_sort |
Zermoglio, Paula Florencia |
| title |
The importance of digitized biocollections as a source of trait data and a new VertNet resource |
| title_short |
The importance of digitized biocollections as a source of trait data and a new VertNet resource |
| title_full |
The importance of digitized biocollections as a source of trait data and a new VertNet resource |
| title_fullStr |
The importance of digitized biocollections as a source of trait data and a new VertNet resource |
| title_full_unstemmed |
The importance of digitized biocollections as a source of trait data and a new VertNet resource |
| title_sort |
importance of digitized biocollections as a source of trait data and a new vertnet resource |
| publishDate |
2016 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17580463_v2016_n_p_Guralnick http://hdl.handle.net/20.500.12110/paper_17580463_v2016_n_p_Guralnick |
| work_keys_str_mv |
AT zermogliopaulaflorencia theimportanceofdigitizedbiocollectionsasasourceoftraitdataandanewvertnetresource AT zermogliopaulaflorencia importanceofdigitizedbiocollectionsasasourceoftraitdataandanewvertnetresource |
| _version_ |
1768545115574370304 |