2025
Brecko, Jonathan; Mathys, Aurore; Chatzinikolaou, Eva; Keklikoglou, Kleoniki; Blettery, Jonathan; Green, Laura; Musson, Alicia; Paton, Alan; Phillips, Sarah; Bastir, Markus; Wiltschke, Karin; Rainer, Heimo; Kroh, Andreas; Haston, Elspeth; Semal, Patrick
DIGIT-KEY: an aid towards uniform 2D+ and 3D digitisation techniques within natural history collections Journal Article
In: European Journal of Taxonomy, vol. 976, pp. 283–298, 2025.
@article{brecko25,
title = {DIGIT-KEY: an aid towards uniform 2D+ and 3D digitisation techniques within natural history collections},
author = {Brecko, Jonathan and Mathys, Aurore and Chatzinikolaou, Eva and Keklikoglou, Kleoniki and Blettery, Jonathan and Green, Laura and Musson, Alicia and Paton, Alan and Phillips, Sarah and Bastir, Markus and Wiltschke, Karin and Rainer, Heimo and Kroh, Andreas and Haston, Elspeth and Semal, Patrick},
url = {https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/2797/12775},
doi = {10.5852/ejt.2025.976.2797},
year = {2025},
date = {2025-02-26},
urldate = {2025-02-26},
journal = {European Journal of Taxonomy},
volume = {976},
pages = {283–298},
abstract = {Natural History institutes hold an immense number of specimens and artefacts. For years these collections were not accessible online, remaining inaccessible to researchers from far away and hidden from the general public. Large digitisation projects and cross-institutional agreements aim to bring their collections into the digital era, such as the SYNTHESYS+ project and the Distributed System of Scientific Collections (DiSSCo) Research Infrastructure. As specimens are 3D physical objects with different characteristics many techniques are available to 3D digitise them. For inexperienced users this can be quite overwhelming. Which techniques are already well tested in other institutions and are suitable for a specific specimen or collection? To investigate this, we have set up a dichotomous identification key for digitisation techniques: DIGIT-KEY, (https://digit.naturalheritage.be/digit-key). For each technique, examples used in SYNTHESYS+ Institutions are visualised and training manuals provided. All information can be easily updated and representatives can be contacted if necessary to request more information about a certain technique. This key can be helpful to achieve comparable results across institutions when digitising collections on demand in future DiSSCo research initiatives coordinated through the European Loans and Visits System (ELViS) for Virtual and Transnational Access.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Natural History institutes hold an immense number of specimens and artefacts. For years these collections were not accessible online, remaining inaccessible to researchers from far away and hidden from the general public. Large digitisation projects and cross-institutional agreements aim to bring their collections into the digital era, such as the SYNTHESYS+ project and the Distributed System of Scientific Collections (DiSSCo) Research Infrastructure. As specimens are 3D physical objects with different characteristics many techniques are available to 3D digitise them. For inexperienced users this can be quite overwhelming. Which techniques are already well tested in other institutions and are suitable for a specific specimen or collection? To investigate this, we have set up a dichotomous identification key for digitisation techniques: DIGIT-KEY, (https://digit.naturalheritage.be/digit-key). For each technique, examples used in SYNTHESYS+ Institutions are visualised and training manuals provided. All information can be easily updated and representatives can be contacted if necessary to request more information about a certain technique. This key can be helpful to achieve comparable results across institutions when digitising collections on demand in future DiSSCo research initiatives coordinated through the European Loans and Visits System (ELViS) for Virtual and Transnational Access.
Antonelli, Alexandre; Teisher, Jordan K; Smith, Rhian J; Ainsworth, A Martyn; Furci, Giuliana; Gaya, Ester; Gonccalves, Susana C; Hawksworth, David L; Larridon, Isabel; Sessa, Emily B; others,
The 2030 Declaration on Scientific Plant and Fungal Collecting Journal Article
In: Plants, People, Planet, vol. 7, no. 1, pp. 11-22, 2025.
@article{antonelli20252030,
title = {The 2030 Declaration on Scientific Plant and Fungal Collecting},
author = {Antonelli, Alexandre and Teisher, Jordan K and Smith, Rhian J and Ainsworth, A Martyn and Furci, Giuliana and Gaya, Ester and Gon{c{c}}alves, Susana C and Hawksworth, David L and Larridon, Isabel and Sessa, Emily B and others},
url = {https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ppp3.10569},
doi = { https://doi.org/10.1002/ppp3.10569},
year = {2025},
date = {2025-01-01},
urldate = {2025-01-01},
journal = {Plants, People, Planet},
volume = {7},
number = {1},
pages = {11-22},
publisher = {Wiley Online Library},
abstract = {Biological samples and their associated information are an essential resource used by scientists, governments, policymakers, practitioners and communities to ensure that biodiversity can be appropriately protected and sustainably used. Yet, considering the enormous task of documenting the vast numbers of as-yet-unknown plant and fungal species, greater international coordination for biological collecting and recording is necessary, built on equitable collecting practices and standards. Here, we propose five commitments to accelerate and enhance scientific knowledge of plant and fungal diversity, while increasing collaboration, benefit sharing and efficiency.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Biological samples and their associated information are an essential resource used by scientists, governments, policymakers, practitioners and communities to ensure that biodiversity can be appropriately protected and sustainably used. Yet, considering the enormous task of documenting the vast numbers of as-yet-unknown plant and fungal species, greater international coordination for biological collecting and recording is necessary, built on equitable collecting practices and standards. Here, we propose five commitments to accelerate and enhance scientific knowledge of plant and fungal diversity, while increasing collaboration, benefit sharing and efficiency.
2024
Güntsch, Anton; Overmann, Jörg; Ebert, Barbara; Bonn, Aletta; Le Bras, Yvan; Engel, Thore; Hovstad, Knut Anders; Lange Canhos, Dora Ann; Newman, Peggy; van Ommen Kloeke, Elaine; others,
National biodiversity data infrastructures: ten essential functions for science, policy, and practice Journal Article
In: BioScience, pp. biae109, 2024.
@article{guntsch2024national,
title = {National biodiversity data infrastructures: ten essential functions for science, policy, and practice},
author = {Güntsch, Anton and Overmann, Jörg and Ebert, Barbara and Bonn, Aletta and Le Bras, Yvan and Engel, Thore and Hovstad, Knut Anders and Lange Canhos, Dora Ann and Newman, Peggy and van Ommen Kloeke, Elaine and others},
doi = {https://doi.org/10.1093/biosci/biae109},
year = {2024},
date = {2024-10-30},
urldate = {2024-10-30},
journal = {BioScience},
pages = {biae109},
publisher = {Oxford University Press},
abstract = {Today, at the international level, powerful data portals are available to biodiversity researchers and policymakers, offering increasingly robust computing and network capacities and capable data services for internationally agreed-on standards. These accelerate individual and complex workflows to map data-driven research processes or even to make them possible for the first time. At the national level, however, and alongside these international developments, national infrastructures are needed to take on tasks that cannot be easily funded or addressed internationally. To avoid gaps, as well as redundancies in the research landscape, national tasks and responsibilities must be clearly defined to align efforts with core priorities. In the present article, we outline 10 essential functions of national biodiversity data infrastructures. They serve as key providers, facilitators, mediators, and platforms for effective biodiversity data management, integration, and analysis that require national efforts to foster biodiversity science, policy, and practice.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Today, at the international level, powerful data portals are available to biodiversity researchers and policymakers, offering increasingly robust computing and network capacities and capable data services for internationally agreed-on standards. These accelerate individual and complex workflows to map data-driven research processes or even to make them possible for the first time. At the national level, however, and alongside these international developments, national infrastructures are needed to take on tasks that cannot be easily funded or addressed internationally. To avoid gaps, as well as redundancies in the research landscape, national tasks and responsibilities must be clearly defined to align efforts with core priorities. In the present article, we outline 10 essential functions of national biodiversity data infrastructures. They serve as key providers, facilitators, mediators, and platforms for effective biodiversity data management, integration, and analysis that require national efforts to foster biodiversity science, policy, and practice.
G. Berendsohn, Walter; Bernal, Silvia Lusa; Hidalgo, Banessa Falcón; Delcid, Dagoberto Rodríguez; W. Moonlight, Peter; Riley Engledow, Henry
Enhancing Herbarium Systems Using Name Matching Mechanisms Journal Article
In: Biodiversity Information Science and Standards , vol. 8, pp. e137867, 2024.
@article{nokey,
title = {Enhancing Herbarium Systems Using Name Matching Mechanisms},
author = {Walter G. Berendsohn and Silvia Lusa Bernal and Banessa Falcón Hidalgo and Dagoberto Rodríguez Delcid and Peter W. Moonlight and Henry Riley Engledow},
doi = {https://doi.org/10.3897/biss.8.137867},
year = {2024},
date = {2024-09-26},
urldate = {2024-09-26},
journal = {Biodiversity Information Science and Standards },
volume = {8},
pages = {e137867},
publisher = {Pensoft Publishers},
abstract = {Virtual aggregators of organism names and taxa play a normative role in consolidating the global biodiversity information infrastructure, serving as resources for researchers worldwide. These aggregators may serve as the glue that binds together local data, ranging from individual researchers' spreadsheets to large databases containing taxonomic checklists for countries or entire regions of the world. The European Union-funded TETTRIs project (Transforming European Taxonomy through Training, Research and Innovations) targets both local data holders and aggregators, aiming to motivate and enable local users to verify their data with the aggregators and, optionally, to link to the aggregators’ services (Berendsohn 2023). It also aims to foster the development of aggregator-side services that streamline usage and facilitate the establishment of such linkages.Here we focus specifically on botanical collection databases, i.e., the plant names contained in herbarium databases. By matching these names to botanical data aggregators like the World Flora Online (WFO) Plant List or the World Checklist of Vascular Plants (WCVP), curators can identify and correct obvious errors in their records. Where an exact match is obtained, the curators can check the aggregator’s opinion about the nomenclatural validity, the taxonomic acceptance and the classification of their name, which may help e.g., in the processing of loan requests. Additionally, by reporting missing or incorrect names or commonly used orthographic variants, curators contribute to improving the overall quality of the infrastructure.There are several services that may be used for name matching. We strongly suggest using the service offered by the WFO Plant List, because the dataset is becoming the most comprehensive global resource for the names of plants (excluding algae). It is inclusive, i.e., it tries to cover all names and name-like designations that have been used in published taxonomic sources. It provides unique, resolvable and stable WFO name identifiers (Miller et al. 2023), and assigns new ones for names that have been corrected. It is supported by a broad spectrum of international botanical institutions (52, up to now). It closely cooperates with existing nomenclators such as Kew’s WCVP, Missouri Botanical Garden’s TROPICOS, and the International Plant Names Index (IPNI). Large parts are edited by TENs (Taxonomic Expert Networks, see Borsch et al. 2020) that may respond to input from users. It provides a unique, stable, resolvable WFO name identifier that can be integrated into local databases and used to follow up on changes made on the aggregator’s side. The data is published under a CC0 rights waiver and the ID connects it to the World Flora Online content website. We looked at specimen occurrence data supplied by herbaria to the Global Biodiversity Information Facility (GBIF). GBIF facilitated a dataset (GBIF.ORG 2024) with a count of specimens for all distinct scientific names in the supplied data for Plantae, plus the name they had matched it to in the GBIF backbone (a pragmatic assemblage of name and taxa from multiple botanical data sources). We filtered out algal groups by selecting only names from Anthocerotophyta, Bryophyta, Marchantiophyta, and Tracheophyta. With the 110,089,964 specimen records came 2,922,635 distinct names. GBIF is taking a number of measures to match names, so that in the end most of the specimens can be assigned to a taxon name in the GBIF backbone. However, we focused on exact literal matches of names, including author abbreviations. Only 681.211 (23.3%) of the uploaded names had an exact match in the GBIF taxonomic backbone, representing 40,401,731 occurrences (36.7% of all). So there is clearly room for improvement.Some measures can be taken on the aggregator’s side to improve the matching process. For example, aggregators should optionally provide exact matches for minor discrepancies in name strings that do not reflect true differences, such as spacing in abbreviated author citations or removing designations like 'spp.' or 'Indet.' to match only the name-citing portion. Other corrections have to be made in the herbarium database itself, e.g., the addition of name authors where these are missing. We found that author citations or the lack of these, represented the main issue of non-exact matching in the data uploaded to GBIF.With local databases and aggregators improving their data and services, a subscription service using aggregator IDs as outlined in Berendsohn 2023 may become a realistic possibility in the near future. TETTRIs is assembling a wish list for aggregator services, which also includes the issues we have identified with the GBIF data submissions. We will further analyse these data and those from the herbaria of the authors' institutions to suggest priorities in data cleaning measures. We will consider how herbarium feedback can be leveraged to enhance aggregator datasets. We will also suggest measures for general collection management systems to facilitate name matching, starting with those used in our herbaria (JACQ, Specify).},
key = { herbarium management system, JACQ, Specify, WFO, WFO Plant List, Catalogue of Life},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Virtual aggregators of organism names and taxa play a normative role in consolidating the global biodiversity information infrastructure, serving as resources for researchers worldwide. These aggregators may serve as the glue that binds together local data, ranging from individual researchers' spreadsheets to large databases containing taxonomic checklists for countries or entire regions of the world. The European Union-funded TETTRIs project (Transforming European Taxonomy through Training, Research and Innovations) targets both local data holders and aggregators, aiming to motivate and enable local users to verify their data with the aggregators and, optionally, to link to the aggregators’ services (Berendsohn 2023). It also aims to foster the development of aggregator-side services that streamline usage and facilitate the establishment of such linkages.Here we focus specifically on botanical collection databases, i.e., the plant names contained in herbarium databases. By matching these names to botanical data aggregators like the World Flora Online (WFO) Plant List or the World Checklist of Vascular Plants (WCVP), curators can identify and correct obvious errors in their records. Where an exact match is obtained, the curators can check the aggregator’s opinion about the nomenclatural validity, the taxonomic acceptance and the classification of their name, which may help e.g., in the processing of loan requests. Additionally, by reporting missing or incorrect names or commonly used orthographic variants, curators contribute to improving the overall quality of the infrastructure.There are several services that may be used for name matching. We strongly suggest using the service offered by the WFO Plant List, because the dataset is becoming the most comprehensive global resource for the names of plants (excluding algae). It is inclusive, i.e., it tries to cover all names and name-like designations that have been used in published taxonomic sources. It provides unique, resolvable and stable WFO name identifiers (Miller et al. 2023), and assigns new ones for names that have been corrected. It is supported by a broad spectrum of international botanical institutions (52, up to now). It closely cooperates with existing nomenclators such as Kew’s WCVP, Missouri Botanical Garden’s TROPICOS, and the International Plant Names Index (IPNI). Large parts are edited by TENs (Taxonomic Expert Networks, see Borsch et al. 2020) that may respond to input from users. It provides a unique, stable, resolvable WFO name identifier that can be integrated into local databases and used to follow up on changes made on the aggregator’s side. The data is published under a CC0 rights waiver and the ID connects it to the World Flora Online content website. We looked at specimen occurrence data supplied by herbaria to the Global Biodiversity Information Facility (GBIF). GBIF facilitated a dataset (GBIF.ORG 2024) with a count of specimens for all distinct scientific names in the supplied data for Plantae, plus the name they had matched it to in the GBIF backbone (a pragmatic assemblage of name and taxa from multiple botanical data sources). We filtered out algal groups by selecting only names from Anthocerotophyta, Bryophyta, Marchantiophyta, and Tracheophyta. With the 110,089,964 specimen records came 2,922,635 distinct names. GBIF is taking a number of measures to match names, so that in the end most of the specimens can be assigned to a taxon name in the GBIF backbone. However, we focused on exact literal matches of names, including author abbreviations. Only 681.211 (23.3%) of the uploaded names had an exact match in the GBIF taxonomic backbone, representing 40,401,731 occurrences (36.7% of all). So there is clearly room for improvement.Some measures can be taken on the aggregator’s side to improve the matching process. For example, aggregators should optionally provide exact matches for minor discrepancies in name strings that do not reflect true differences, such as spacing in abbreviated author citations or removing designations like 'spp.' or 'Indet.' to match only the name-citing portion. Other corrections have to be made in the herbarium database itself, e.g., the addition of name authors where these are missing. We found that author citations or the lack of these, represented the main issue of non-exact matching in the data uploaded to GBIF.With local databases and aggregators improving their data and services, a subscription service using aggregator IDs as outlined in Berendsohn 2023 may become a realistic possibility in the near future. TETTRIs is assembling a wish list for aggregator services, which also includes the issues we have identified with the GBIF data submissions. We will further analyse these data and those from the herbaria of the authors' institutions to suggest priorities in data cleaning measures. We will consider how herbarium feedback can be leveraged to enhance aggregator datasets. We will also suggest measures for general collection management systems to facilitate name matching, starting with those used in our herbaria (JACQ, Specify).
Schiller, Edmund; Wiltschke-Schrotta, Karin; Häffner, Eva; Buschbom, Jutta; Leliaert, Frederik; Zimkus, Breda; Dickie, John; Gomes, Suzete; Lyal, Chris; Mulcahy, Daniel; others,
Permits, contracts and their terms for biodiversity specimens Journal Article
In: Research Ideas and Outcomes, vol. 10, pp. e114366, 2024.
@article{schiller2024permits,
title = {Permits, contracts and their terms for biodiversity specimens},
author = {Schiller, Edmund and Wiltschke-Schrotta, Karin and Häffner, Eva and Buschbom, Jutta and Leliaert, Frederik and Zimkus, Breda and Dickie, John and Gomes, Suzete and Lyal, Chris and Mulcahy, Daniel and others},
doi = {https://doi.org/10.3897/rio.10.e114366},
year = {2024},
date = {2024-01-10},
urldate = {2024-01-10},
journal = {Research Ideas and Outcomes},
volume = {10},
pages = {e114366},
publisher = {Pensoft Publishers},
abstract = {We present two different typologies of legal/contractual information in the context of natural history objects: the Biodiversity Permit/Contract Typology categorises permits and contracts, and the Typology of Legal/Contractual Terms for Biodiversity Specimens categorises the terms within permits and contracts. The Typologies have been developed under the EU-funded SYNTHESYS+ project with the participation of experts from outside the consortium. The document further addresses a possible technical integration of these typologies into the Distributed System of Scientific Collections (DiSSCo). The implementation in the DiSSCo data model is outlined and a concrete use case is presented to show how conditions, e.g. the Typology of Legal/Contractual Terms, can be introduced into the DiSSCo Electronic Loans and Visits System (ElViS). Finally, we give an outlook on the next steps to develop the typologies into a standard that supports compliance with legal and contractual obligations within the wider community of natural science collections.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We present two different typologies of legal/contractual information in the context of natural history objects: the Biodiversity Permit/Contract Typology categorises permits and contracts, and the Typology of Legal/Contractual Terms for Biodiversity Specimens categorises the terms within permits and contracts. The Typologies have been developed under the EU-funded SYNTHESYS+ project with the participation of experts from outside the consortium. The document further addresses a possible technical integration of these typologies into the Distributed System of Scientific Collections (DiSSCo). The implementation in the DiSSCo data model is outlined and a concrete use case is presented to show how conditions, e.g. the Typology of Legal/Contractual Terms, can be introduced into the DiSSCo Electronic Loans and Visits System (ElViS). Finally, we give an outlook on the next steps to develop the typologies into a standard that supports compliance with legal and contractual obligations within the wider community of natural science collections.
2023
Rainer, Heimo; Berger, Andreas; M. Schuster, Tanja; Walter, Johannes; Reich, Dieter; Zernig, Kurt; Danihelka, Jiří; Galušková, Hana; Mráz, Patrik; Tkach, Natalia; Hentschel, Jörn; Müller, Jochen; Wagner, Sarah; Berendsohn, Walter; Lücking, Robert; Vogt, Robert; Pignotti, Lia; Roma-Marzio, Francesco; Peruzzi, Lorenzo
Community Curation of Nomenclatural and Taxonomic Information in the Context of the Collection Management System JACQ Journal Article
In: Biodiversity Information Science and Standards, vol. 7, pp. e112571, 2023, ( ).
@article{Rainer2023,
title = {Community Curation of Nomenclatural and Taxonomic Information in the Context of the Collection Management System JACQ},
author = {Heimo Rainer and Andreas Berger and Tanja M. Schuster and Johannes Walter and Dieter Reich and Kurt Zernig and Jiří Danihelka and Hana Galušková and Patrik Mráz and Natalia Tkach and Jörn Hentschel and Jochen Müller and Sarah Wagner and Walter Berendsohn and Robert Lücking and Robert Vogt and Lia Pignotti and Francesco Roma-Marzio and Lorenzo Peruzzi},
doi = {https://doi.org/10.3897/biss.7.112571},
year = {2023},
date = {2023-09-12},
urldate = {2023-09-12},
journal = {Biodiversity Information Science and Standards},
volume = {7},
pages = {e112571},
abstract = {Nomenclatural and taxonomic information are crucial for curating botanical collections. In the course of changing methods for systematic and taxonomic studies, classification systems changed considerably over time (Dalla Torre and Harms 1900, Durand and Bentham 1888, Endlicher 1836, Angiosperm Phylogeny Group et al. 2016). Various approaches to store preserved material have been implemented, most of them based on scientific names (e.g., families, genera, species) often in combination with other criteria such as geographic provenance or collectors.
The collection management system, JACQ, was established in the early 2000s then developed to support multiple institutions. It features a centralised data storage (with mirror sites) and access via the Internet. Participating collections can download their data at any time in a comma-separated values (CSV) format. From the beginning, JACQ was conceived as a collaboration platform for objects housed in botanical collections, i.e., plant, fungal and algal groups. For these groups, various sources of taxonomic reference exist, nowadays online resources are preferred, e.g., Catalogue of Life, AlgaeBase, Index Fungorum, Mycobank, Tropicos, Plants of the World Online, International Plant Names Index (IPNI), World Flora Online, Euro+Med, Anthos, Flora of Northamerica, REFLORA, Flora of China, Flora of Cuba, Australian Virtual Herbarium (AVH).
Implementation and (re)use of PIDs
Persistent identifiers (PIDs) for names (at any taxonomic rank) apart from PIDs for taxa, are essential to allow and support reliable referencing across institutions and thematic research networks (Agosti et al. 2022). For this purpose we have integrated referencing to several of the above mentioned resources and populate the names used inside JACQ with those external PIDs. For example, Salix rosmarinifolia is accepted in Plants of the World Online while Euro+Med Plantbase considers it a synonym of Salix repens subsp. rosmarinifolia. Either one can be an identification of a specimen in the JACQ database.
Retrieval of collection material
One strong use case is the curation of material in historic collections. On the basis of outdated taxon concepts that were applied to the material in history, "old" synonyms are omnipresent in historical collections. In order to retrieve all material of a given taxon, it is necessary to know all relevant names.
Future outlook
In combination with the capability of Linked Data and the IIIF (International Image Interoperability Framework) technology, these PIDs serve as crucial elements for the integration of decentralized information systems and reuse of (global) taxonomic backbones in combination with collection management systems (Gamer and Kreyenbühl 2022, Hyam 2022, Loh 2017).
},
key = {nomenclature, floras, taxonomy, PID, linked data, IIIF},
note = {
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nomenclatural and taxonomic information are crucial for curating botanical collections. In the course of changing methods for systematic and taxonomic studies, classification systems changed considerably over time (Dalla Torre and Harms 1900, Durand and Bentham 1888, Endlicher 1836, Angiosperm Phylogeny Group et al. 2016). Various approaches to store preserved material have been implemented, most of them based on scientific names (e.g., families, genera, species) often in combination with other criteria such as geographic provenance or collectors.
The collection management system, JACQ, was established in the early 2000s then developed to support multiple institutions. It features a centralised data storage (with mirror sites) and access via the Internet. Participating collections can download their data at any time in a comma-separated values (CSV) format. From the beginning, JACQ was conceived as a collaboration platform for objects housed in botanical collections, i.e., plant, fungal and algal groups. For these groups, various sources of taxonomic reference exist, nowadays online resources are preferred, e.g., Catalogue of Life, AlgaeBase, Index Fungorum, Mycobank, Tropicos, Plants of the World Online, International Plant Names Index (IPNI), World Flora Online, Euro+Med, Anthos, Flora of Northamerica, REFLORA, Flora of China, Flora of Cuba, Australian Virtual Herbarium (AVH).
Implementation and (re)use of PIDs
Persistent identifiers (PIDs) for names (at any taxonomic rank) apart from PIDs for taxa, are essential to allow and support reliable referencing across institutions and thematic research networks (Agosti et al. 2022). For this purpose we have integrated referencing to several of the above mentioned resources and populate the names used inside JACQ with those external PIDs. For example, Salix rosmarinifolia is accepted in Plants of the World Online while Euro+Med Plantbase considers it a synonym of Salix repens subsp. rosmarinifolia. Either one can be an identification of a specimen in the JACQ database.
Retrieval of collection material
One strong use case is the curation of material in historic collections. On the basis of outdated taxon concepts that were applied to the material in history, "old" synonyms are omnipresent in historical collections. In order to retrieve all material of a given taxon, it is necessary to know all relevant names.
Future outlook
In combination with the capability of Linked Data and the IIIF (International Image Interoperability Framework) technology, these PIDs serve as crucial elements for the integration of decentralized information systems and reuse of (global) taxonomic backbones in combination with collection management systems (Gamer and Kreyenbühl 2022, Hyam 2022, Loh 2017).
The collection management system, JACQ, was established in the early 2000s then developed to support multiple institutions. It features a centralised data storage (with mirror sites) and access via the Internet. Participating collections can download their data at any time in a comma-separated values (CSV) format. From the beginning, JACQ was conceived as a collaboration platform for objects housed in botanical collections, i.e., plant, fungal and algal groups. For these groups, various sources of taxonomic reference exist, nowadays online resources are preferred, e.g., Catalogue of Life, AlgaeBase, Index Fungorum, Mycobank, Tropicos, Plants of the World Online, International Plant Names Index (IPNI), World Flora Online, Euro+Med, Anthos, Flora of Northamerica, REFLORA, Flora of China, Flora of Cuba, Australian Virtual Herbarium (AVH).
Implementation and (re)use of PIDs
Persistent identifiers (PIDs) for names (at any taxonomic rank) apart from PIDs for taxa, are essential to allow and support reliable referencing across institutions and thematic research networks (Agosti et al. 2022). For this purpose we have integrated referencing to several of the above mentioned resources and populate the names used inside JACQ with those external PIDs. For example, Salix rosmarinifolia is accepted in Plants of the World Online while Euro+Med Plantbase considers it a synonym of Salix repens subsp. rosmarinifolia. Either one can be an identification of a specimen in the JACQ database.
Retrieval of collection material
One strong use case is the curation of material in historic collections. On the basis of outdated taxon concepts that were applied to the material in history, "old" synonyms are omnipresent in historical collections. In order to retrieve all material of a given taxon, it is necessary to know all relevant names.
Future outlook
In combination with the capability of Linked Data and the IIIF (International Image Interoperability Framework) technology, these PIDs serve as crucial elements for the integration of decentralized information systems and reuse of (global) taxonomic backbones in combination with collection management systems (Gamer and Kreyenbühl 2022, Hyam 2022, Loh 2017).
K Miller, Chuck; Berendsohn, Walter; Ulate, William; Hyam, Roger
WFO-IDs: Unique identifiers for all known plants managed by the World Flora Online Conference
vol. 7, 2023.
@conference{K Miller2023,
title = {WFO-IDs: Unique identifiers for all known plants managed by the World Flora Online},
author = {Chuck K Miller and Walter Berendsohn and William Ulate and Roger Hyam},
doi = {10.3897/biss.7.111210},
year = {2023},
date = {2023-08-17},
urldate = {2023-08-17},
journal = {Biodiversity Information Science and Standards},
volume = {7},
pages = {e111210},
abstract = {The World Flora Online (WFO) project (Borsch et al. 2020) was initiated in 2012 in response to Target 1 of the Global Strategy for Plant Conservation*1, "To create an online flora of all known plants by 2020" (Wyse Jackson and Kennedy 2009). A WFO Consortium of over 40 international institutions has been formed. The World Flora Online Public Portal*2 is built upon a taxonomic backbone of plant taxonomic data that integrates the International Plant Name Index (IPNI)*3, World Checklist of Vascular Plants (WCVP)*4, Tropicos*5, Angiosperm Phylogeny Group 4*6, Pteridophyte Phylogeny Group (PPG I 2016), supplemented by the Global Compositae Checklist*7, Solanaceae Source*8, and others. To facilitate the ongoing curation of the WFO backbone, identifiers called WFO-IDs have been created for each of the over 1.59 million names included in WFO. WFO-IDs are comprehensive for all known plants, both vascular and non-vascular except algae. IPNI-IDs are limited to vascular plants and do not give the current taxonomic status of the name. WFO-IDs also cover invalid designations, i.e., some effectively published “names” like orthographic variants that have been used in taxonomic literature, so that their invalid status is made explicit. WFO IDs follow FAIR principles (Findable, Accessible, Interoperable, and Reusable). Relationships between WFO-IDs are also recorded by the WFO Taxonomic Backbone, including synonymy and homonymy, and are accessible via the WFO Portal. WFO is continuously updating the taxonomic backbone by engagement of new plant Taxonomic Expert Networks (TENs) focused on selected plant groups. WFO also includes over 500,000 descriptive data items gathered from digital floras and monographs, and other sources. Descriptive data can be text descriptions, images, geographic distributions, identification keys, phylogenetic trees, threat status, lifeform or habitat. Descriptive data records are all assigned a WFO-ID, if they are new to WFO, by a name matching process with the WFO Taxonomic Backbone. A new tool called Rhakhis (Hyam et al. 2022), developed at Royal Botanic Garden, Edinburgh, is used to manage the WFO Taxonomic Backbone data and includes APIs to access the versioned backbone data. This presentation will review the origins and history of WFO-IDs and how they are being used for the World Flora Online.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
The World Flora Online (WFO) project (Borsch et al. 2020) was initiated in 2012 in response to Target 1 of the Global Strategy for Plant Conservation*1, "To create an online flora of all known plants by 2020" (Wyse Jackson and Kennedy 2009). A WFO Consortium of over 40 international institutions has been formed. The World Flora Online Public Portal*2 is built upon a taxonomic backbone of plant taxonomic data that integrates the International Plant Name Index (IPNI)*3, World Checklist of Vascular Plants (WCVP)*4, Tropicos*5, Angiosperm Phylogeny Group 4*6, Pteridophyte Phylogeny Group (PPG I 2016), supplemented by the Global Compositae Checklist*7, Solanaceae Source*8, and others. To facilitate the ongoing curation of the WFO backbone, identifiers called WFO-IDs have been created for each of the over 1.59 million names included in WFO. WFO-IDs are comprehensive for all known plants, both vascular and non-vascular except algae. IPNI-IDs are limited to vascular plants and do not give the current taxonomic status of the name. WFO-IDs also cover invalid designations, i.e., some effectively published “names” like orthographic variants that have been used in taxonomic literature, so that their invalid status is made explicit. WFO IDs follow FAIR principles (Findable, Accessible, Interoperable, and Reusable). Relationships between WFO-IDs are also recorded by the WFO Taxonomic Backbone, including synonymy and homonymy, and are accessible via the WFO Portal. WFO is continuously updating the taxonomic backbone by engagement of new plant Taxonomic Expert Networks (TENs) focused on selected plant groups. WFO also includes over 500,000 descriptive data items gathered from digital floras and monographs, and other sources. Descriptive data can be text descriptions, images, geographic distributions, identification keys, phylogenetic trees, threat status, lifeform or habitat. Descriptive data records are all assigned a WFO-ID, if they are new to WFO, by a name matching process with the WFO Taxonomic Backbone. A new tool called Rhakhis (Hyam et al. 2022), developed at Royal Botanic Garden, Edinburgh, is used to manage the WFO Taxonomic Backbone data and includes APIs to access the versioned backbone data. This presentation will review the origins and history of WFO-IDs and how they are being used for the World Flora Online.
Berendsohn, Walter G.
vol. 7, no. e109666, 2023.
@conference{Berendsohn2023,
title = {Use Cases for Scientific Name Identifiers and Name Matching: Progress report from the TETTRIs project},
author = {Walter G. Berendsohn},
doi = {10.3897/biss.7.109666},
year = {2023},
date = {2023-07-21},
urldate = {2023-07-21},
journal = {Biodiversity Information Science and Standards},
volume = {7},
number = {e109666},
abstract = {One of the tasks of the EU TETTRIs (Transforming European Taxonomy through Training, Research and Innovations) project is to document and enhance the mapping of local taxon lists (or scientific data holdings containing lists of taxon names) to global and European aggregators of scientific names and taxa. Local lists are here understood to range from spreadsheets maintained by individual researchers to large databases containing taxonomic checklists for countries or entire regions of the world (e.g., the European plant checklist Euro+Med PlantBase). Unique and resolvable name identifiers (IDs) play a central role, because they allow tracking of name usage in the target aggregator. Aggregators should (and some do) provide name matching services that provide stable resolvable name IDs that users may incorporate into their databases. So, why would the administrators of such local lists want to relate their name data to global aggregators, for example to Catalogue of Life, World Flora Online or EU-Nomen? We are collecting such use cases and from those we will propose mechanisms to improve name matching and other services provided by the target aggregator systems. Simple use cases such as checking the names of a local list of insects against the names in the normative European EU-Nomen checklist (a.k.a. Pan European Species Infrastructure PESI) are already largely covered by existing name checking mechanisms. They are often used to detect orthographical or taxonomic errors. On the other hand, a common use case in the elaboration of taxonomic treatments with comprehensive cover of the names in the taxonomic group is to identify existing names that have to be investigated for that purpose, i.e., to identify names held by the aggregator that are not already in the treatment. Currently, this use case is not covered by a simple mechanism or service. Another common use case is that local data portals include links to aggregator databases when displaying a name (e.g., Tropicos). This allows linking to the name record in the target aggregator and thus (directly or indirectly), to the target's current or versioned taxonomic concept related to the specific name, and its opinion regarding the nomenclatural status. However, this is accomplished by using the name string as the search parameter, which may or may not work correctly. In contrast, the incorporation of the target aggregator's resolvable ID in the local database establishes an unequivocal link between the local name and the name in the aggregator treatment. This brings about an improvement in data quality for such links. Beyond that, users who did match their names should have the possibility to use a "taxon concept subscription" to be automatically informed of changes in the name usage of their names. This implies that target aggregators of taxonomic data trace changes in the concepts of the taxon where they place a respective name. These may be changes in status (accepted name to synonym or vice-versa) but also the addition of new synonyms to the concept, or the removal of synonyms. We hope that TETTRIs can instigate the implementation of taxon concept subscriptions by target aggregators. Nomenclators (databases that do not treat the taxonomic status of a name) would have to trace changes in nomenclatural notes or status of the name. In the two years remaining for this task in the TETTRIs project, we will continue to test and document services provided by the aggregators and promote the usage of name IDs in local systems and publications, in order to contribute to a linked data landscape for biodiversity information.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
One of the tasks of the EU TETTRIs (Transforming European Taxonomy through Training, Research and Innovations) project is to document and enhance the mapping of local taxon lists (or scientific data holdings containing lists of taxon names) to global and European aggregators of scientific names and taxa. Local lists are here understood to range from spreadsheets maintained by individual researchers to large databases containing taxonomic checklists for countries or entire regions of the world (e.g., the European plant checklist Euro+Med PlantBase). Unique and resolvable name identifiers (IDs) play a central role, because they allow tracking of name usage in the target aggregator. Aggregators should (and some do) provide name matching services that provide stable resolvable name IDs that users may incorporate into their databases. So, why would the administrators of such local lists want to relate their name data to global aggregators, for example to Catalogue of Life, World Flora Online or EU-Nomen? We are collecting such use cases and from those we will propose mechanisms to improve name matching and other services provided by the target aggregator systems. Simple use cases such as checking the names of a local list of insects against the names in the normative European EU-Nomen checklist (a.k.a. Pan European Species Infrastructure PESI) are already largely covered by existing name checking mechanisms. They are often used to detect orthographical or taxonomic errors. On the other hand, a common use case in the elaboration of taxonomic treatments with comprehensive cover of the names in the taxonomic group is to identify existing names that have to be investigated for that purpose, i.e., to identify names held by the aggregator that are not already in the treatment. Currently, this use case is not covered by a simple mechanism or service. Another common use case is that local data portals include links to aggregator databases when displaying a name (e.g., Tropicos). This allows linking to the name record in the target aggregator and thus (directly or indirectly), to the target's current or versioned taxonomic concept related to the specific name, and its opinion regarding the nomenclatural status. However, this is accomplished by using the name string as the search parameter, which may or may not work correctly. In contrast, the incorporation of the target aggregator's resolvable ID in the local database establishes an unequivocal link between the local name and the name in the aggregator treatment. This brings about an improvement in data quality for such links. Beyond that, users who did match their names should have the possibility to use a "taxon concept subscription" to be automatically informed of changes in the name usage of their names. This implies that target aggregators of taxonomic data trace changes in the concepts of the taxon where they place a respective name. These may be changes in status (accepted name to synonym or vice-versa) but also the addition of new synonyms to the concept, or the removal of synonyms. We hope that TETTRIs can instigate the implementation of taxon concept subscriptions by target aggregators. Nomenclators (databases that do not treat the taxonomic status of a name) would have to trace changes in nomenclatural notes or status of the name. In the two years remaining for this task in the TETTRIs project, we will continue to test and document services provided by the aggregators and promote the usage of name IDs in local systems and publications, in order to contribute to a linked data landscape for biodiversity information.
Park, Daniel S.; Feng, Xiao Feng; Akiyama, Shinobu; et alia,
The colonial legacy of herbaria Journal Article
In: Nature Human Behaviour, iss. 2023, 2023.
@article{Park2023,
title = {The colonial legacy of herbaria},
author = {Daniel S. Park and Xiao Feng Feng and Shinobu Akiyama and et alia},
url = {https://www.biorxiv.org/content/early/2021/11/02/2021.10.27.466174.full.pdf},
doi = {https://doi.org/10.1038/s41562-023-01616-7},
year = {2023},
date = {2023-06-12},
urldate = {2023-06-12},
journal = {Nature Human Behaviour},
issue = {2023},
abstract = {Herbarium collections shape our understanding of Earth’s flora and are crucial for addressing global change issues. Their formation, however, is not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the Global North, the extent and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Herbarium collections shape our understanding of Earth’s flora and are crucial for addressing global change issues. Their formation, however, is not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the Global North, the extent and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.
2022
Hardisty, Alex R; Ellwood, Elizabeth R; Nelson, Gil; Zimkus, Breda; Buschbom, Jutta; Addink, Wouter; Rabeler, Richard K; Bates, John; Bentley, Andrew; others,
Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet Journal Article
In: BioScience, vol. 72, iss. 10, pp. 978–987, 2022.
@article{hardisty2022digital,
title = {Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet},
author = {Hardisty, Alex R and Ellwood, Elizabeth R and Nelson, Gil and Zimkus, Breda and Buschbom, Jutta and Addink, Wouter and Rabeler, Richard K and Bates, John and Bentley, Andrew and others},
doi = { https://doi.org/10.1093/biosci/biac060},
year = {2022},
date = {2022-08-03},
urldate = {2022-08-03},
journal = {BioScience},
volume = {72},
issue = {10},
pages = {978–987},
abstract = {The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.
2021
Güntsch, Anton; Groom, Quentin; Ernst, Marcus; Holetschek, Jörg; Plank, Andreas; Röpert, Dominik; Fichtmüller, David; Shorthouse, David Peter; Hyam, Roger; Dillen, Mathias; Trekels, Maarten; Haston, Elspeth; Rainer, Heimo
A botanical demonstration of the potential of linking data using unique identifiers for people Journal Article
In: PLOS ONE, vol. 16, no. 12, pp. 1-11, 2021.
@article{10.1371/journal.pone.0261130,
title = {A botanical demonstration of the potential of linking data using unique identifiers for people},
author = {Anton Güntsch and Quentin Groom and Marcus Ernst and Jörg Holetschek and Andreas Plank and Dominik Röpert and David Fichtmüller and David Peter Shorthouse and Roger Hyam and Mathias Dillen and Maarten Trekels and Elspeth Haston and Heimo Rainer},
url = {https://doi.org/10.1371/journal.pone.0261130},
doi = {10.1371/journal.pone.0261130},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {PLOS ONE},
volume = {16},
number = {12},
pages = {1-11},
publisher = {Public Library of Science},
abstract = {Natural history collection data available digitally on the web have so far only made limited use of the potential of semantic links among themselves and with cross-disciplinary resources. In a pilot study, botanical collections of the Consortium of European Taxonomic Facilities (CETAF) have therefore begun to semantically annotate their collection data, starting with data on people, and to link them via a central index system. As a result, it is now possible to query data on collectors across different collections and automatically link them to a variety of external resources. The system is being continuously developed and is already in production use in an international collection portal.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Natural history collection data available digitally on the web have so far only made limited use of the potential of semantic links among themselves and with cross-disciplinary resources. In a pilot study, botanical collections of the Consortium of European Taxonomic Facilities (CETAF) have therefore begun to semantically annotate their collection data, starting with data on people, and to link them via a central index system. As a result, it is now possible to query data on collectors across different collections and automatically link them to a variety of external resources. The system is being continuously developed and is already in production use in an international collection portal.
Abgaz, Yalemisew; Souza, Renato Rocha; Methuku, Japesh; Koch, Gerda; Dorn, Amelie
A Methodology for Semantic Enrichment of Cultural Heritage Images Using Artificial Intelligence Technologies Journal Article
In: Journal of Imaging, vol. 7, no. 8, 2021, ISSN: 2313-433X.
@article{jimaging7080121,
title = {A Methodology for Semantic Enrichment of Cultural Heritage Images Using Artificial Intelligence Technologies},
author = {Yalemisew Abgaz and Renato Rocha Souza and Japesh Methuku and Gerda Koch and Amelie Dorn},
url = {https://www.mdpi.com/2313-433X/7/8/121},
doi = {10.3390/jimaging7080121},
issn = {2313-433X},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Journal of Imaging},
volume = {7},
number = {8},
abstract = {Cultural heritage images are among the primary media for communicating and preserving the cultural values of a society. The images represent concrete and abstract content and symbolise the social, economic, political, and cultural values of the society. However, an enormous amount of such values embedded in the images is left unexploited partly due to the absence of methodological and technical solutions to capture, represent, and exploit the latent information. With the emergence of new technologies and availability of cultural heritage images in digital formats, the methodology followed to semantically enrich and utilise such resources become a vital factor in supporting users need. This paper presents a methodology proposed to unearth the cultural information communicated via cultural digital images by applying Artificial Intelligence (AI) technologies (such as Computer Vision (CV) and semantic web technologies). To this end, the paper presents a methodology that enables efficient analysis and enrichment of a large collection of cultural images covering all the major phases and tasks. The proposed method is applied and tested using a case study on cultural image collections from the Europeana platform. The paper further presents the analysis of the case study, the challenges, the lessons learned, and promising future research areas on the topic.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cultural heritage images are among the primary media for communicating and preserving the cultural values of a society. The images represent concrete and abstract content and symbolise the social, economic, political, and cultural values of the society. However, an enormous amount of such values embedded in the images is left unexploited partly due to the absence of methodological and technical solutions to capture, represent, and exploit the latent information. With the emergence of new technologies and availability of cultural heritage images in digital formats, the methodology followed to semantically enrich and utilise such resources become a vital factor in supporting users need. This paper presents a methodology proposed to unearth the cultural information communicated via cultural digital images by applying Artificial Intelligence (AI) technologies (such as Computer Vision (CV) and semantic web technologies). To this end, the paper presents a methodology that enables efficient analysis and enrichment of a large collection of cultural images covering all the major phases and tasks. The proposed method is applied and tested using a case study on cultural image collections from the Europeana platform. The paper further presents the analysis of the case study, the challenges, the lessons learned, and promising future research areas on the topic.
2020
Groom, Quentin; Güntsch, Anton; Huybrechts, Pieter; Kearney, Nicole; Leachman, Siobhan; Nicolson, Nicky; Page, Roderic DM; Shorthouse, David P; Thessen, Anne E; Haston, Elspeth
People are essential to linking biodiversity data Journal Article
In: Database, vol. 2020, pp. baaa072, 2020.
@article{groom2020people,
title = {People are essential to linking biodiversity data},
author = {Groom, Quentin and Güntsch, Anton and Huybrechts, Pieter and Kearney, Nicole and Leachman, Siobhan and Nicolson, Nicky and Page, Roderic DM and Shorthouse, David P and Thessen, Anne E and Haston, Elspeth},
doi = {https://doi.org/10.1093/database/baaa072},
year = {2020},
date = {2020-11-27},
urldate = {2020-11-27},
journal = {Database},
volume = {2020},
pages = {baaa072},
publisher = {Oxford University Press UK},
abstract = {People are one of the best known and most stable entities in the biodiversity knowledge graph. The wealth of public information associated with people and the ability to identify them uniquely open up the possibility to make more use of these data in biodiversity science. Person data are almost always associated with entities such as specimens, molecular sequences, taxonomic names, observations, images, traits and publications. For example, the digitization and the aggregation of specimen data from museums and herbaria allow us to view a scientist’s specimen collecting in conjunction with the whole corpus of their works. However, the metadata of these entities are also useful in validating data, integrating data across collections and institutional databases and can be the basis of future research into biodiversity and science. In addition, the ability to reliably credit collectors for their work has the potential to change the incentive structure to promote improved curation and maintenance of natural history collections.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
People are one of the best known and most stable entities in the biodiversity knowledge graph. The wealth of public information associated with people and the ability to identify them uniquely open up the possibility to make more use of these data in biodiversity science. Person data are almost always associated with entities such as specimens, molecular sequences, taxonomic names, observations, images, traits and publications. For example, the digitization and the aggregation of specimen data from museums and herbaria allow us to view a scientist’s specimen collecting in conjunction with the whole corpus of their works. However, the metadata of these entities are also useful in validating data, integrating data across collections and institutional databases and can be the basis of future research into biodiversity and science. In addition, the ability to reliably credit collectors for their work has the potential to change the incentive structure to promote improved curation and maintenance of natural history collections.
Wouter Addink,; Hardisty, Alex
‘openDS’–progress on the new standard for digital specimens Conference
vol. 4, 2020.
@conference{addink2020opends,
title = {‘openDS’–progress on the new standard for digital specimens},
author = {Addink, Wouter, and Alex Hardisty},
doi = {doi.org/10.3897/biss.4.59338},
year = {2020},
date = {2020-10-06},
urldate = {2020-10-06},
journal = {Biodiversity Information Science and Standards},
volume = {4},
pages = {e59338},
abstract = {In a Biodiversity_Next 2019 symposium, a vision of Digital Specimens based on the concept of a Digital Object Architecture (Kahn and Wilensky 2006) (DOA) was discussed as a new layer between data infrastructure of natural science collections and user applications for processing and interacting with information about specimens and collections. This vision would enable the transformation of institutional curatorial practises into joint community curation of the scientific data by providing seamless global access to specimens and collections spanning multiple collection-holding institutions and sources. A DOA-based implementation (Lannom et al. 2020) also offers wider, more flexible, and ‘FAIR’ (Findable, Accessible, Interoperable, Reusable) access for varied research and policy uses: recognising curatorial work, annotating with latest taxonomic treatments, understanding variations, working with DNA sequences or chemical analyses, supporting regulatory processes for health, food, security, sustainability and environmental change, inventions/products critical to the bio-economy, and educational uses. To make this vision a reality, a specification is needed that describes what a Digital Specimen is, and how to technically implement it. This specification is named 'openDS' for open Digital Specimen. It needs to describe how machines and humans can act on a Digital Specimen and gain attribution for their work; how the data can be serialized and packaged; and it needs to describe the object model (the scientific content part and its structure). The object model should describe how to include the specimen data itself as well as all data derived from the specimen, which is in principle the same as what the Extended Specimen model aims to describe. This part will therefore be developed in close collaboration with people working on that model. After the Biodiversity_Next symposium, the idea of a standard for Digital Specimens has been further discussed and detailed in a MOBILISE Workshop in Warsaw, 2020, with stakeholders like the GBIF, iDigBio, CETAF and DiSSCo. The workshop examined the technical basis of the new specification, agreed on scope and structure of the new specification and laid groundwork for future activities in the Research Data Alliance (RDA), Biodiversity Information Standards (TDWG), and technical workshops. A working group in the DiSSCo Prepare project has begun on the technical specification of the ‘open Digital Specimen’ (openDS). This specification will provide the definition of what a Digital Specimen is, its logical structure and content, and the operations permitted on that. The group is also working on a document with frequently asked questions. Realising the vision of Digital Specimen on a global level requires openDS to become a new TDWG standard and to be aligned with the vision for Extended Specimens. A TDWG Birds-of-a-Feather working session in September 2020 discusses and plans this further. The object model will include concepts from ABCD 3.0 and EFG extension for geo-sciences, and also extend from bco:MaterialSample in the OBO Foundry’s Biological Collection Ontology (BCO), which is linked to Darwin Core and from iao:InformationContentEntity in OBO Foundry's Information Artifact Ontology (IAO). openDS will also make use of the RDA/TDWG attribution metadata recommendation and other RDA recommendations. A publication is in preparation that describes the relationship with RDA recommendations in more detail, which will also be presented in the TDWG symposium.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
In a Biodiversity_Next 2019 symposium, a vision of Digital Specimens based on the concept of a Digital Object Architecture (Kahn and Wilensky 2006) (DOA) was discussed as a new layer between data infrastructure of natural science collections and user applications for processing and interacting with information about specimens and collections. This vision would enable the transformation of institutional curatorial practises into joint community curation of the scientific data by providing seamless global access to specimens and collections spanning multiple collection-holding institutions and sources. A DOA-based implementation (Lannom et al. 2020) also offers wider, more flexible, and ‘FAIR’ (Findable, Accessible, Interoperable, Reusable) access for varied research and policy uses: recognising curatorial work, annotating with latest taxonomic treatments, understanding variations, working with DNA sequences or chemical analyses, supporting regulatory processes for health, food, security, sustainability and environmental change, inventions/products critical to the bio-economy, and educational uses. To make this vision a reality, a specification is needed that describes what a Digital Specimen is, and how to technically implement it. This specification is named 'openDS' for open Digital Specimen. It needs to describe how machines and humans can act on a Digital Specimen and gain attribution for their work; how the data can be serialized and packaged; and it needs to describe the object model (the scientific content part and its structure). The object model should describe how to include the specimen data itself as well as all data derived from the specimen, which is in principle the same as what the Extended Specimen model aims to describe. This part will therefore be developed in close collaboration with people working on that model. After the Biodiversity_Next symposium, the idea of a standard for Digital Specimens has been further discussed and detailed in a MOBILISE Workshop in Warsaw, 2020, with stakeholders like the GBIF, iDigBio, CETAF and DiSSCo. The workshop examined the technical basis of the new specification, agreed on scope and structure of the new specification and laid groundwork for future activities in the Research Data Alliance (RDA), Biodiversity Information Standards (TDWG), and technical workshops. A working group in the DiSSCo Prepare project has begun on the technical specification of the ‘open Digital Specimen’ (openDS). This specification will provide the definition of what a Digital Specimen is, its logical structure and content, and the operations permitted on that. The group is also working on a document with frequently asked questions. Realising the vision of Digital Specimen on a global level requires openDS to become a new TDWG standard and to be aligned with the vision for Extended Specimens. A TDWG Birds-of-a-Feather working session in September 2020 discusses and plans this further. The object model will include concepts from ABCD 3.0 and EFG extension for geo-sciences, and also extend from bco:MaterialSample in the OBO Foundry’s Biological Collection Ontology (BCO), which is linked to Darwin Core and from iao:InformationContentEntity in OBO Foundry's Information Artifact Ontology (IAO). openDS will also make use of the RDA/TDWG attribution metadata recommendation and other RDA recommendations. A publication is in preparation that describes the relationship with RDA recommendations in more detail, which will also be presented in the TDWG symposium.
2019
Holetschek, Jörg
Taxonomies for Natural History Collections Online
Europeana, (Ed.): 2019, visited: 31.10.2019.
@online{nokey,
title = {Taxonomies for Natural History Collections},
author = {Jörg Holetschek},
editor = {Europeana},
url = {https://pro.europeana.eu/post/taxonomies-for-natural-history-collections},
year = {2019},
date = {2019-10-31},
urldate = {2019-10-31},
abstract = {
Presenting digital collections of natural history has its own unique set of challenges. This is something that Europeana's natural history aggregator OpenUp! knows well. With almost 9 million objects on Europeana Collections - visibility and search come with some very specific parameters. The below explores some of these key elements behind presenting natural history objects online and lets you know the best ways to find what you are looking for.},
keywords = {},
pubstate = {published},
tppubtype = {online}
}
Presenting digital collections of natural history has its own unique set of challenges. This is something that Europeana's natural history aggregator OpenUp! knows well. With almost 9 million objects on Europeana Collections - visibility and search come with some very specific parameters. The below explores some of these key elements behind presenting natural history objects online and lets you know the best ways to find what you are looking for.
Blum, Stanley; Barker, Katharine; Baskauf, Steven J; Berendsohn, Walter G.; Buttigieg, Pier Luigi; Döring, Markus; Droege, Gabriele; Fichtmueller, David; Glöckler, Falko; Güntsch, Anton; Guralnick, Robert; Hoffmann, Jana; Klazenga, Niels; Macklin, James; Morris, Paul J.; Paul, Deborah L; Petersen, Mareike; Robertson, Tim; Sachs, Joel; Peter Shorthouse, David; Walls, Ramona; Wieczorek, John; F Zermoglio, Paula F
Integrating ABCD and DarwinCore: Toward a better foundation for biodiversity information standards Conference
vol. 3, Pensoft Publishers, 2019.
@conference{biss.3.37491,
title = {Integrating ABCD and DarwinCore: Toward a better foundation for biodiversity information standards},
author = {Stanley Blum and Katharine Barker and Steven J Baskauf and Walter G. Berendsohn and Pier Luigi Buttigieg and Markus Döring and Gabriele Droege and David Fichtmueller and Falko Glöckler and Anton Güntsch and Robert Guralnick and Jana Hoffmann and Niels Klazenga and James Macklin and Paul J. Morris and Deborah L Paul and Mareike Petersen and Tim Robertson and Joel Sachs and David Peter Shorthouse and Ramona Walls and John Wieczorek and Paula F F Zermoglio},
doi = {https://doi.org/10.3897/biss.3.37491},
year = {2019},
date = {2019-07-02},
urldate = {2019-07-02},
volume = {3},
publisher = {Pensoft Publishers},
abstract = {For the last 15 years, Biodiversity Information Standards (TDWG) has recognized two competing standards for organism occurrence data, ABCD (Access to Biological Collections Data; Holetschek et al. 2012) and DarwinCore (Wieczorek et al. 2012). These two representations emerged from contrasting strategies for mobilizing information about organism occurrences (also commonly called species occurrence data). ABCD was capable of representing details of more kinds of information, but was necessarily more complicated. DarwinCore, on the other hand, was simpler but more limited in its ability to represent data of different kinds and formats. TDWG endorsed both standards because the different projects and communities that generated them remained dedicated to their different strategies and tool sets, and the Global Biodiversity Information Facility (GBIF) developed the ability to integrate data published in either standard.
Since their inceptions, DarwinCore and ABCD have become more similar. DarwinCore has gotten more complicated through the addition of terms and has begun to assign terms to classes. ABCD is now expressed in RDF (Resource Description Framework), potentially enabling re-use of terms with alternative structures among classes. At the same time, methodologies for conceptual modeling and representing complex scientific data have continued to evolve. In particular, a suite of modeling and data representation methods related to linked data and the semantic web, i.e., RDF, SKOS (Simple Knowledge Organization System), and OWL (web Ontology Language), promise to make it easier for us to reconcile shared concepts among different representations or schemas.
A mapping between ABCD 2.1 and DarwinCore has existed since before 2005.*1 ABCD 3.0 and DarwinCore are both now represented in RDF. 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. Reconciling ABCD and DarwinCore through alignment with BCO (in the OBO Foundry; Smith et al. 2007) would better connect TDWG standards to other domains in biology. We appreciate that many working scientists and data managers perceive ontologies as overly complicated. To mitigate the steep learning curve associated with ontologies, we expect to create simpler application profiles or schemas to guide and serve narrower communities of practice within the wider biodiversity domain. We also plan to integrate the current work of the Taxonomic Names and Concepts Interest Group and thereby eliminate the redundancy between DarwinCore and Taxonomic Concepts Transfer Schema (TCS; Kennedy et al. 2006).
At the time of this writing, we have only agreements from the authors (i.e., conveners of relevant TDWG Interest Groups and other key stakeholders) to collaborate in pursuit of these common goals. In this presentation we will give a more detailed description of our objectives and products, the methods we are using to achieve them, and our progress to date.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
For the last 15 years, Biodiversity Information Standards (TDWG) has recognized two competing standards for organism occurrence data, ABCD (Access to Biological Collections Data; Holetschek et al. 2012) and DarwinCore (Wieczorek et al. 2012). These two representations emerged from contrasting strategies for mobilizing information about organism occurrences (also commonly called species occurrence data). ABCD was capable of representing details of more kinds of information, but was necessarily more complicated. DarwinCore, on the other hand, was simpler but more limited in its ability to represent data of different kinds and formats. TDWG endorsed both standards because the different projects and communities that generated them remained dedicated to their different strategies and tool sets, and the Global Biodiversity Information Facility (GBIF) developed the ability to integrate data published in either standard.
Since their inceptions, DarwinCore and ABCD have become more similar. DarwinCore has gotten more complicated through the addition of terms and has begun to assign terms to classes. ABCD is now expressed in RDF (Resource Description Framework), potentially enabling re-use of terms with alternative structures among classes. At the same time, methodologies for conceptual modeling and representing complex scientific data have continued to evolve. In particular, a suite of modeling and data representation methods related to linked data and the semantic web, i.e., RDF, SKOS (Simple Knowledge Organization System), and OWL (web Ontology Language), promise to make it easier for us to reconcile shared concepts among different representations or schemas.
A mapping between ABCD 2.1 and DarwinCore has existed since before 2005.*1 ABCD 3.0 and DarwinCore are both now represented in RDF. 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. Reconciling ABCD and DarwinCore through alignment with BCO (in the OBO Foundry; Smith et al. 2007) would better connect TDWG standards to other domains in biology. We appreciate that many working scientists and data managers perceive ontologies as overly complicated. To mitigate the steep learning curve associated with ontologies, we expect to create simpler application profiles or schemas to guide and serve narrower communities of practice within the wider biodiversity domain. We also plan to integrate the current work of the Taxonomic Names and Concepts Interest Group and thereby eliminate the redundancy between DarwinCore and Taxonomic Concepts Transfer Schema (TCS; Kennedy et al. 2006).
At the time of this writing, we have only agreements from the authors (i.e., conveners of relevant TDWG Interest Groups and other key stakeholders) to collaborate in pursuit of these common goals. In this presentation we will give a more detailed description of our objectives and products, the methods we are using to achieve them, and our progress to date.
Since their inceptions, DarwinCore and ABCD have become more similar. DarwinCore has gotten more complicated through the addition of terms and has begun to assign terms to classes. ABCD is now expressed in RDF (Resource Description Framework), potentially enabling re-use of terms with alternative structures among classes. At the same time, methodologies for conceptual modeling and representing complex scientific data have continued to evolve. In particular, a suite of modeling and data representation methods related to linked data and the semantic web, i.e., RDF, SKOS (Simple Knowledge Organization System), and OWL (web Ontology Language), promise to make it easier for us to reconcile shared concepts among different representations or schemas.
A mapping between ABCD 2.1 and DarwinCore has existed since before 2005.*1 ABCD 3.0 and DarwinCore are both now represented in RDF. 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. Reconciling ABCD and DarwinCore through alignment with BCO (in the OBO Foundry; Smith et al. 2007) would better connect TDWG standards to other domains in biology. We appreciate that many working scientists and data managers perceive ontologies as overly complicated. To mitigate the steep learning curve associated with ontologies, we expect to create simpler application profiles or schemas to guide and serve narrower communities of practice within the wider biodiversity domain. We also plan to integrate the current work of the Taxonomic Names and Concepts Interest Group and thereby eliminate the redundancy between DarwinCore and Taxonomic Concepts Transfer Schema (TCS; Kennedy et al. 2006).
At the time of this writing, we have only agreements from the authors (i.e., conveners of relevant TDWG Interest Groups and other key stakeholders) to collaborate in pursuit of these common goals. In this presentation we will give a more detailed description of our objectives and products, the methods we are using to achieve them, and our progress to date.
Hardisty, Alex; Ma, Keping; Nelson, Gil; Fortes, Jose
‘openDS’ – A New Standard for Digital Specimens and Other Natural Science Digital Object Types Conference
vol. 3, Pensoft Publishers, 2019.
@conference{hardisty2019opends,
title = {‘openDS’ – A New Standard for Digital Specimens and Other Natural Science Digital Object Types},
author = {Hardisty, Alex and Ma, Keping and Nelson, Gil and Fortes, Jose},
doi = {https://doi.org/10.3897/biss.3.37033},
year = {2019},
date = {2019-06-18},
urldate = {2019-06-18},
journal = {Biodiversity Information Science and Standards},
volume = {3},
pages = {e37033},
publisher = {Pensoft Publishers},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
2017
Koch, Gerda; Koch, Walter
Aggregation und Management von Metadaten im Kontext von Europeana Journal Article
In: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2, pp. 170–178, 2017.
@article{Koch_Koch_2017,
title = {Aggregation und Management von Metadaten im Kontext von Europeana},
author = {Gerda Koch and Walter Koch},
url = {https://journals.univie.ac.at/index.php/voebm/article/view/2071},
doi = {10.31263/voebm.v70i2.1776},
year = {2017},
date = {2017-09-01},
urldate = {2017-09-01},
journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare},
volume = {70},
number = {2},
pages = {170–178},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Roger Hyam Anton Güntsch, Gregor Hagedorn
Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects Journal Article
In: Database, vol. 2017, pp. bax003, 2017.
@article{guntsch2017actionable,
title = {Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects},
author = {Anton Güntsch, Roger Hyam, Gregor Hagedorn, Simon Chagnoux, Dominik Röpert, Ana Casino, Gabi Droege, Falko Glöckler, Karsten Gödderz, Quentin Groom, Jana Hoffmann, Ayco Holleman, Matúš Kempa, Hanna Koivula, Karol Marhold, Nicky Nicolson, Vincent S. Smith, Dagmar Triebel},
doi = {https://doi.org/10.1093/database/bax003},
year = {2017},
date = {2017-01-11},
urldate = {2017-01-11},
journal = {Database},
volume = {2017},
pages = {bax003},
publisher = {Oxford University Press},
abstract = {With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals.
2016
Holetschek, Jörg; Baumann, Gisela; Koch, Gerda; Berendsohn, Walter G.
Natural History in Europeana - Accessing Scientific Collection Objects via LOD Proceedings Article
In: Garoufallou, Emmanouel; Coll, Imma Subirats; Stellato, Armando; Greenberg, Jane (Ed.): Metadata and Semantics Research, pp. 223–234, Springer International Publishing, Cham, 2016, ISBN: 978-3-319-49157-8.
@inproceedings{10.1007/978-3-319-49157-8_20,
title = {Natural History in Europeana - Accessing Scientific Collection Objects via LOD},
author = {Jörg Holetschek and Gisela Baumann and Gerda Koch and Walter G. Berendsohn},
editor = {Emmanouel Garoufallou and Imma Subirats Coll and Armando Stellato and Jane Greenberg},
doi = {10.1007/978-3-319-49157-8_20},
isbn = {978-3-319-49157-8},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
booktitle = {Metadata and Semantics Research},
pages = {223--234},
publisher = {Springer International Publishing},
address = {Cham},
abstract = {Millions of specimens housed in collections of natural history institutions document our planet's biodiversity over centuries and represent both an indispensable knowledge base for today's biological research as well as a cultural heritage. Digitization efforts of the past years have produced a substantial amount of digital assets: high-resolution images, videos, sound files, 3D imagery and 3D models. The OpenUp! Natural History Aggregator draws together these virtual representations of specimens from a multitude of institutions and feeds them into Europeana, the cross-domain portal for Europe's digitized cultural heritage. Enriching their metadata with data drawn from additional resources such as common names, taxonomic literature and geographic terms helps to increase discoverability und usability. The assignment of stable uniform resource locators and the application of standard vocabularies, existing ontologies and frameworks like RDF allow effective linking of web resources from different knowledge domains, thus creating linked open data.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Millions of specimens housed in collections of natural history institutions document our planet's biodiversity over centuries and represent both an indispensable knowledge base for today's biological research as well as a cultural heritage. Digitization efforts of the past years have produced a substantial amount of digital assets: high-resolution images, videos, sound files, 3D imagery and 3D models. The OpenUp! Natural History Aggregator draws together these virtual representations of specimens from a multitude of institutions and feeds them into Europeana, the cross-domain portal for Europe's digitized cultural heritage. Enriching their metadata with data drawn from additional resources such as common names, taxonomic literature and geographic terms helps to increase discoverability und usability. The assignment of stable uniform resource locators and the application of standard vocabularies, existing ontologies and frameworks like RDF allow effective linking of web resources from different knowledge domains, thus creating linked open data.
2014
Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; others,
Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies Journal Article
In: PloS one, vol. 9, no. 3, pp. e89606, 2014.
@article{walls2014semantics,
title = {Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies},
author = {Walls, Ramona L and Deck, John and Guralnick, Robert and Baskauf, Steve and Beaman, Reed and Blum, Stanley and Bowers, Shawn and Buttigieg, Pier Luigi and Davies, Neil and Endresen, Dag and others},
doi = {https://doi.org/10.1371/journal.pone.0089606},
year = {2014},
date = {2014-03-03},
urldate = {2014-03-03},
journal = {PloS one},
volume = {9},
number = {3},
pages = {e89606},
publisher = {Public Library of Science San Francisco, USA},
abstract = {The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.
2012
Holetschek, J.; Dröge, G.; Güntsch, A.; Berendsohn, W. G.
The ABCD of primary biodiversity data access Journal Article
In: Plant Biosystems - An International Journal Dealing with All Aspects of Plant Biology, vol. 146, no. 4, pp. 771–779, 2012.
@article{holetschek2012abcd,
title = {The ABCD of primary biodiversity data access},
author = {Holetschek, J. and Dröge, G. and Güntsch, A. and Berendsohn, W. G.},
doi = {https://doi.org/10.1080/11263504.2012.740085},
year = {2012},
date = {2012-10-16},
urldate = {2012-10-16},
journal = {Plant Biosystems - An International Journal Dealing with All Aspects of Plant Biology},
volume = {146},
number = {4},
pages = {771–779},
publisher = {Taylor & Francis},
abstract = {Within the context of the Global Biodiversity Information Facility (GBIF), the Biological Collections Access Service (BioCASe) has been set up to foment data provision by natural history content providers. Products include the BioCASe Protocol and the PyWrapper software, a web service allowing to access rich natural history data using complex schemas like ABCD (Access to Biological Collection Data). New developments include the possibility to produce DarwinCore-Archive files using PyWrapper, in order to facilitate the indexing of large datasets by aggregators such as GBIF. However, BioCASe continues to be committed to distributed data access and continues to provide the possibility to directly query the web service for up-to-date data directly from the provider's database. ABCD provides comprehensive coverage of natural history data, and has been extended to cover DNA collections (ABCD-DNA) and geosciences (ABCD-EFG, the extension for geosciences). BioCASe also developed web portal software that allows to access and display rich data provided by special interest networks. We posit that the XML-based networking approach using a highly standardised data definition such as ABCD continues to be a valuable approach towards mobilising natural history information. Some suggestions are made regarding further improvements of ABCD.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Within the context of the Global Biodiversity Information Facility (GBIF), the Biological Collections Access Service (BioCASe) has been set up to foment data provision by natural history content providers. Products include the BioCASe Protocol and the PyWrapper software, a web service allowing to access rich natural history data using complex schemas like ABCD (Access to Biological Collection Data). New developments include the possibility to produce DarwinCore-Archive files using PyWrapper, in order to facilitate the indexing of large datasets by aggregators such as GBIF. However, BioCASe continues to be committed to distributed data access and continues to provide the possibility to directly query the web service for up-to-date data directly from the provider's database. ABCD provides comprehensive coverage of natural history data, and has been extended to cover DNA collections (ABCD-DNA) and geosciences (ABCD-EFG, the extension for geosciences). BioCASe also developed web portal software that allows to access and display rich data provided by special interest networks. We posit that the XML-based networking approach using a highly standardised data definition such as ABCD continues to be a valuable approach towards mobilising natural history information. Some suggestions are made regarding further improvements of ABCD.
