The document discusses issues in providing access to biological specimen data through the Global Biodiversity Information Facility (GBIF). As GBIF has scaled up, it has had to address challenges around scale, geospatial integration, and taxonomic integration. GBIF now uses Darwin Core Archives as a scalable publishing standard, integrates national shapefiles to verify geospatial coordinates, and provides taxonomic data to help reconcile heterogeneous classifications across datasets. These approaches have helped GBIF effectively grow its network from 70 million records in 2007 to over 300 million records today.
The document summarizes a meeting about the Global Names Architecture (GNA) in Paris, France. It discusses developing common standards and services to enable global discovery of taxonomic and nomenclatural resources. This includes creating a Global Names Index and registry to reconcile names across resources and promote sharing data in consistent, integrated ways. The Integrated Publishing Toolkit and Darwin Core Archives are proposed as part of the architecture to publish and share species checklists and metadata.
Biodiversity informatics describes integrating biological research, computational science, and software engineering to deal with biotic data. Biodiversity data is used for taxonomy, biogeography, ecology, conservation and more. Data is collected, standardized, digitized and published using Darwin Core and made available through organizations like GBIF. Key challenges include dealing with synonyms and standardizing data across sources.
The document discusses challenges related to the use of scientific names in biodiversity informatics. It outlines objectives for the Global Names Architecture (GNA) to address issues like name variations, synonyms, homonyms, and differing taxonomic views. The GNA aims to create a complete index of all scientific names linked to species information, reconciled to an authoritative nomenclatural dictionary. It also aims to provide multiple taxonomic classifications and lists that are openly accessible and can effectively organize species data to support discovery.
This document summarizes a NISO webinar on guidelines and resources for developing data access plans in response to the Office of Science and Technology Policy's (OSTP) 2013 memo. The memo directs large federal funding agencies to develop public access plans for research results. The webinar outlines the required elements of these plans and provides existing guidelines and resources that can help agencies meet digital data requirements, such as standards for data dissemination, description, and long-term preservation. Speakers from the Interuniversity Consortium for Political and Social Research discuss how agencies can leverage existing infrastructure and best practices to develop plans that maximize access to and reuse of federal research data.
Knowledge Organization System (KOS) for biodiversity information resources, G...Dag Endresen
Slides from a presentation on the Knowledge Organization System (KOS) work program for GBIF. KOS developments for biodiversity information resources and input to the emerging Vocabulary Management Task Group (VoMaG).
Links
GBIF KOS prototype tools, http://kos.gbif.org/
Tool: Semantic Wiki prototype, http://terms.gbif.org/wiki/
Tool: ISOcat prototype demo, http://kos.gbif.org/isocat/
GBIF concept vocabulary term browser, http://kos.gbif.org/termbrowser/
GBIF Resources Repository, http://rs.gbif.org/terms/
GBIF Vocabulary Server, http://vocabularies.gbif.org/
GBIF Resources Browser, http://tools.gbif.org/resource-browser/
The document discusses issues in providing access to biological specimen data through the Global Biodiversity Information Facility (GBIF). As GBIF has scaled up, it has had to address challenges around scale, geospatial integration, and taxonomic integration. GBIF now uses Darwin Core Archives as a scalable publishing standard, integrates national shapefiles to verify geospatial coordinates, and provides taxonomic data to help reconcile heterogeneous classifications across datasets. These approaches have helped GBIF effectively grow its network from 70 million records in 2007 to over 300 million records today.
The document summarizes a meeting about the Global Names Architecture (GNA) in Paris, France. It discusses developing common standards and services to enable global discovery of taxonomic and nomenclatural resources. This includes creating a Global Names Index and registry to reconcile names across resources and promote sharing data in consistent, integrated ways. The Integrated Publishing Toolkit and Darwin Core Archives are proposed as part of the architecture to publish and share species checklists and metadata.
Biodiversity informatics describes integrating biological research, computational science, and software engineering to deal with biotic data. Biodiversity data is used for taxonomy, biogeography, ecology, conservation and more. Data is collected, standardized, digitized and published using Darwin Core and made available through organizations like GBIF. Key challenges include dealing with synonyms and standardizing data across sources.
The document discusses challenges related to the use of scientific names in biodiversity informatics. It outlines objectives for the Global Names Architecture (GNA) to address issues like name variations, synonyms, homonyms, and differing taxonomic views. The GNA aims to create a complete index of all scientific names linked to species information, reconciled to an authoritative nomenclatural dictionary. It also aims to provide multiple taxonomic classifications and lists that are openly accessible and can effectively organize species data to support discovery.
This document summarizes a NISO webinar on guidelines and resources for developing data access plans in response to the Office of Science and Technology Policy's (OSTP) 2013 memo. The memo directs large federal funding agencies to develop public access plans for research results. The webinar outlines the required elements of these plans and provides existing guidelines and resources that can help agencies meet digital data requirements, such as standards for data dissemination, description, and long-term preservation. Speakers from the Interuniversity Consortium for Political and Social Research discuss how agencies can leverage existing infrastructure and best practices to develop plans that maximize access to and reuse of federal research data.
Knowledge Organization System (KOS) for biodiversity information resources, G...Dag Endresen
Slides from a presentation on the Knowledge Organization System (KOS) work program for GBIF. KOS developments for biodiversity information resources and input to the emerging Vocabulary Management Task Group (VoMaG).
Links
GBIF KOS prototype tools, http://kos.gbif.org/
Tool: Semantic Wiki prototype, http://terms.gbif.org/wiki/
Tool: ISOcat prototype demo, http://kos.gbif.org/isocat/
GBIF concept vocabulary term browser, http://kos.gbif.org/termbrowser/
GBIF Resources Repository, http://rs.gbif.org/terms/
GBIF Vocabulary Server, http://vocabularies.gbif.org/
GBIF Resources Browser, http://tools.gbif.org/resource-browser/
Per de Place Bjørn - Revolutionizing taxonomy through an open-access web-regi...ICZN
The document discusses how the Global Biodiversity Information Facility (GBIF) and ZooBank can collaborate to enhance taxonomy. It proposes using globally unique identifiers (GUIDs) to disseminate ZooBank entries through the GBIF portal and network. This would help make ZooBank data more available and allow specimens associated with ZooBank entries to be referenced through GUIDs. The document also discusses enabling retrospective registration of nomenclatural data in ZooBank via GBIF data providers and making ZooBank available to species pages/banks.
This document provides a summary of a framework for managing vocabularies as presented at the TDWG Vocabulary Management Task Group meeting. It discusses the status of TDWG ontologies, requirements for a vocabulary management framework, and Semantic MediaWiki as a potential platform for collaborative vocabulary development. Key points include:
- Vocabularies are a core component of the TDWG technical architecture and provide shared understanding of terms, but development and governance has been challenging.
- A framework is needed to standardize the process for minting terms, releasing finalized concept vocabularies, and reusing terms in other schemas and ontologies to promote interoperability.
- Semantic MediaWiki is proposed as a platform for collaborative
Global Biodiversity Information Facility - 2013Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF), GBIF-Norway and the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken) at the Norwegian Institute for Forestry and Landscape (Skog og Landskap) at Ås outside Oslo on the 17th October 2013. Seminar together with the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken).
Introduction to GBIF. GBIF seminar in Bergen. 2016-12-14Dag Endresen
GBIF Norway provides a summary of biodiversity data publishing and access activities in Norway through the Global Biodiversity Information Facility (GBIF). Over 22 million occurrence records with locations in Norway have been published through GBIF from 31 countries worldwide. The GBIF node team at the University of Oslo works to publish Norwegian biodiversity data and facilitate its use. They collaborate with other Norwegian institutions like Artsdatabanken and NTNU University Museum to advance open data policies and research utilizing GBIF.
The Dryad Digital Repository: Published evolutionary data as part of the gre...Todd Vision
The Dryad Digital Repository aims to publish evolutionary data as part of the greater data ecosystem. Its goals are to publish data reported in biological literature, promote data reuse, and ensure responsible long-term data stewardship through a consortium of journals. Archiving data at publication is most effective for reuse and preservation. A survey found most researchers agree data should be publicly accessible, though opinions varied on whether it should be required or voluntary. Lessons learned indicate the importance of journals in data publication, the value of shared public repositories, and achieving a balance of benefit and burden for data authors.
Keynote presented to KE workshop held in conjunction with the release of the report "A Surfboard for Riding the Wave
Towards a four country action programme on research data": http://www.knowledge-exchange.info/Default.aspx?ID=469
Lecture for a course at NTNU, 27th January 2021
CC-BY 4.0 Dag Endresen https://orcid.org/0000-0002-2352-5497
See also http://bit.ly/biodiversityinformatics
https://www.gbif.no/events/2021/lecture-ntnu-gbif.html
GBIF and reuse of research data, Bergen (2016-12-14)Dag Endresen
Biodiversity informatics seminar at the Department of Biology, University of Bergen on data publication and reuse of GBIF-mediated biodiversity data on 14th December 2016. Organized by the Norwegian GBIF Node and the Norwegian Biodiversity Information Center (NBIC, Artsdatabanken).
See also: http://www.gbif.no/events/2016/data-publishing-seminar-in-bergen.html
See also: http://doi.org/10.13140/RG.2.2.24290.32969
Global Biodiversity Information Facility (GBIF) - 2012Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF) and GBIF Norway for the Department of Technical and Scientific Conservation (CONSERV) at the Natural History Museum, University of Oslo. Tøyen, Oslo, 7 November 2012.
Leveraging publication metadata to help overcome the data ingest bottleneck Todd Vision
This document discusses leveraging publication metadata to help address the data ingest bottleneck in scientific publishing. It proposes integrating data submission with manuscript submission to journals to make data archiving integral to the publication process. This integrated approach would help overcome issues around orphan data and allow linking of publications to underlying data through identifiers. Benefits include increased data findability, reuse, and credit to data creators. Challenges include gaining widespread adoption among journals and developers.
The role of biodiversity informatics in GBIF, 2021-05-18Dag Endresen
The document discusses the role of biodiversity informatics and the Global Biodiversity Information Facility (GBIF) in making biodiversity data available through open access. GBIF provides free and open access to over 1.6 billion species occurrence records from over 1600 data publishers. The document highlights how digitizing natural history collections and integrating diverse biodiversity data sources can support research and policy goals. It emphasizes best practices like using common data standards, publishing datasets on GBIF to make them widely discoverable and reusable, and citing data with DOIs to incentivize open data sharing.
EURISCO demo installations of IPT, at GBIF EU Nodes meeting in Alicante (11 M...Dag Endresen
Regional GBIF NODES meeting of Europe in March 2010. Presentation of current activities from the NordGen NODE. Implementations of the GBIF IPT toolkit for genebanks in Europe. Upgrade for selected genebanks from the BioCASE publishing toolkit to the IPT. First step of a scheduled larger implementation planned to start in 2011 as part of the EuroGeneBank application pending EU funding decision. NordGen IPT EURISCO
Data reuse and scholarly reward: understanding practice and building infrastr...Todd Vision
This document discusses a study analyzing data reuse across scientific repositories. It finds that open gene expression data receives 69% more citations on average than closed data. It also finds patterns of data reuse vary across repositories, with references managers, blogs, bookmarks, and social networks all being venues for citations beyond traditional publications. The document advocates moving beyond traditional metrics like citations and journal impact factors to more fully capture the impact of open data sharing.
Biodiversity Informatics: An Interdisciplinary ChallengeBryan Heidorn
"Impacto de la Informática en el Conocimiento de la Biodiversidad: Actualidad y Futuro” at Universidad Nacional de Colombia on August 12, 2011. https://sites.google.com/site/simposioinformaticaicn/home
GBIF data publishing. GBIF seminar in Bergen. 2016-12-14Dag Endresen
GBIF data publishing seminar at the Department for Biology at the University of Bergen. http://www.gbif.no/events/2016/data-publishing-seminar-in-bergen.html
GBIF is a global biodiversity data infrastructure that provides open access to over 1.6 billion species occurrence records. It connects over 1,600 data publishers through a voluntary network of participants and aims to facilitate research and policy related to biodiversity and sustainable development. Data shared through GBIF is cited with digital object identifiers to give credit to data publishers and encourage further data sharing. The presentation reviewed GBIF's role in open science and data citation principles, provided statistics on global and Norwegian contributions to the network, and explained how to publish and cite biodiversity data through GBIF.
The document discusses Plazi's work on converting biodiversity literature into structured data through text mining and markup. Key points include:
- Plazi extracts scientific names, tables, references and geographic data from literature and converts it into semantically enriched text and RDF.
- Their pipelines currently have over 50,000 taxonomic treatments life and are providing data to databases like NCBI, GBIF and EOL.
- Future plans include collaborating with ContentMine for daily treatment extraction, releasing RDF and text mining versions 1.0, and expanding the biodiversity literature repository to 100,000 references.
Lecture presented at the Journals Club of the Naturhistorisches Museum Bern, March 17, 2014.
"Towards an (European) Open Biodiversity Knowledge Management System"
Per de Place Bjørn - Revolutionizing taxonomy through an open-access web-regi...ICZN
The document discusses how the Global Biodiversity Information Facility (GBIF) and ZooBank can collaborate to enhance taxonomy. It proposes using globally unique identifiers (GUIDs) to disseminate ZooBank entries through the GBIF portal and network. This would help make ZooBank data more available and allow specimens associated with ZooBank entries to be referenced through GUIDs. The document also discusses enabling retrospective registration of nomenclatural data in ZooBank via GBIF data providers and making ZooBank available to species pages/banks.
This document provides a summary of a framework for managing vocabularies as presented at the TDWG Vocabulary Management Task Group meeting. It discusses the status of TDWG ontologies, requirements for a vocabulary management framework, and Semantic MediaWiki as a potential platform for collaborative vocabulary development. Key points include:
- Vocabularies are a core component of the TDWG technical architecture and provide shared understanding of terms, but development and governance has been challenging.
- A framework is needed to standardize the process for minting terms, releasing finalized concept vocabularies, and reusing terms in other schemas and ontologies to promote interoperability.
- Semantic MediaWiki is proposed as a platform for collaborative
Global Biodiversity Information Facility - 2013Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF), GBIF-Norway and the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken) at the Norwegian Institute for Forestry and Landscape (Skog og Landskap) at Ås outside Oslo on the 17th October 2013. Seminar together with the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken).
Introduction to GBIF. GBIF seminar in Bergen. 2016-12-14Dag Endresen
GBIF Norway provides a summary of biodiversity data publishing and access activities in Norway through the Global Biodiversity Information Facility (GBIF). Over 22 million occurrence records with locations in Norway have been published through GBIF from 31 countries worldwide. The GBIF node team at the University of Oslo works to publish Norwegian biodiversity data and facilitate its use. They collaborate with other Norwegian institutions like Artsdatabanken and NTNU University Museum to advance open data policies and research utilizing GBIF.
The Dryad Digital Repository: Published evolutionary data as part of the gre...Todd Vision
The Dryad Digital Repository aims to publish evolutionary data as part of the greater data ecosystem. Its goals are to publish data reported in biological literature, promote data reuse, and ensure responsible long-term data stewardship through a consortium of journals. Archiving data at publication is most effective for reuse and preservation. A survey found most researchers agree data should be publicly accessible, though opinions varied on whether it should be required or voluntary. Lessons learned indicate the importance of journals in data publication, the value of shared public repositories, and achieving a balance of benefit and burden for data authors.
Keynote presented to KE workshop held in conjunction with the release of the report "A Surfboard for Riding the Wave
Towards a four country action programme on research data": http://www.knowledge-exchange.info/Default.aspx?ID=469
Lecture for a course at NTNU, 27th January 2021
CC-BY 4.0 Dag Endresen https://orcid.org/0000-0002-2352-5497
See also http://bit.ly/biodiversityinformatics
https://www.gbif.no/events/2021/lecture-ntnu-gbif.html
GBIF and reuse of research data, Bergen (2016-12-14)Dag Endresen
Biodiversity informatics seminar at the Department of Biology, University of Bergen on data publication and reuse of GBIF-mediated biodiversity data on 14th December 2016. Organized by the Norwegian GBIF Node and the Norwegian Biodiversity Information Center (NBIC, Artsdatabanken).
See also: http://www.gbif.no/events/2016/data-publishing-seminar-in-bergen.html
See also: http://doi.org/10.13140/RG.2.2.24290.32969
Global Biodiversity Information Facility (GBIF) - 2012Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF) and GBIF Norway for the Department of Technical and Scientific Conservation (CONSERV) at the Natural History Museum, University of Oslo. Tøyen, Oslo, 7 November 2012.
Leveraging publication metadata to help overcome the data ingest bottleneck Todd Vision
This document discusses leveraging publication metadata to help address the data ingest bottleneck in scientific publishing. It proposes integrating data submission with manuscript submission to journals to make data archiving integral to the publication process. This integrated approach would help overcome issues around orphan data and allow linking of publications to underlying data through identifiers. Benefits include increased data findability, reuse, and credit to data creators. Challenges include gaining widespread adoption among journals and developers.
The role of biodiversity informatics in GBIF, 2021-05-18Dag Endresen
The document discusses the role of biodiversity informatics and the Global Biodiversity Information Facility (GBIF) in making biodiversity data available through open access. GBIF provides free and open access to over 1.6 billion species occurrence records from over 1600 data publishers. The document highlights how digitizing natural history collections and integrating diverse biodiversity data sources can support research and policy goals. It emphasizes best practices like using common data standards, publishing datasets on GBIF to make them widely discoverable and reusable, and citing data with DOIs to incentivize open data sharing.
EURISCO demo installations of IPT, at GBIF EU Nodes meeting in Alicante (11 M...Dag Endresen
Regional GBIF NODES meeting of Europe in March 2010. Presentation of current activities from the NordGen NODE. Implementations of the GBIF IPT toolkit for genebanks in Europe. Upgrade for selected genebanks from the BioCASE publishing toolkit to the IPT. First step of a scheduled larger implementation planned to start in 2011 as part of the EuroGeneBank application pending EU funding decision. NordGen IPT EURISCO
Data reuse and scholarly reward: understanding practice and building infrastr...Todd Vision
This document discusses a study analyzing data reuse across scientific repositories. It finds that open gene expression data receives 69% more citations on average than closed data. It also finds patterns of data reuse vary across repositories, with references managers, blogs, bookmarks, and social networks all being venues for citations beyond traditional publications. The document advocates moving beyond traditional metrics like citations and journal impact factors to more fully capture the impact of open data sharing.
Biodiversity Informatics: An Interdisciplinary ChallengeBryan Heidorn
"Impacto de la Informática en el Conocimiento de la Biodiversidad: Actualidad y Futuro” at Universidad Nacional de Colombia on August 12, 2011. https://sites.google.com/site/simposioinformaticaicn/home
GBIF data publishing. GBIF seminar in Bergen. 2016-12-14Dag Endresen
GBIF data publishing seminar at the Department for Biology at the University of Bergen. http://www.gbif.no/events/2016/data-publishing-seminar-in-bergen.html
GBIF is a global biodiversity data infrastructure that provides open access to over 1.6 billion species occurrence records. It connects over 1,600 data publishers through a voluntary network of participants and aims to facilitate research and policy related to biodiversity and sustainable development. Data shared through GBIF is cited with digital object identifiers to give credit to data publishers and encourage further data sharing. The presentation reviewed GBIF's role in open science and data citation principles, provided statistics on global and Norwegian contributions to the network, and explained how to publish and cite biodiversity data through GBIF.
The document discusses Plazi's work on converting biodiversity literature into structured data through text mining and markup. Key points include:
- Plazi extracts scientific names, tables, references and geographic data from literature and converts it into semantically enriched text and RDF.
- Their pipelines currently have over 50,000 taxonomic treatments life and are providing data to databases like NCBI, GBIF and EOL.
- Future plans include collaborating with ContentMine for daily treatment extraction, releasing RDF and text mining versions 1.0, and expanding the biodiversity literature repository to 100,000 references.
Lecture presented at the Journals Club of the Naturhistorisches Museum Bern, March 17, 2014.
"Towards an (European) Open Biodiversity Knowledge Management System"
DOI and the Mitteilungen: communicating scientific results in the futureagosti
lecture presented at Ento.CH, Neuchâtel, Switzerland; March 4, 2016. Developing a scenario for the future of the Mitteilungen der Schweizerischen Entomologischen Gesellschaft into the direction of semantically enhanced publications.
Data Sharing Principles and Legal Interoperability for Essential Biodiversity...agosti
The document discusses principles of open data sharing and legal interoperability of research data. It provides summaries of the GEO Data Sharing Principles from 2005 and a proposed updated version from 2015. The principles advocate sharing data as open data by default without charge or reuse restrictions. Exceptions can be made for reasons of national security, endangered species protection, or other restrictions allowed by law. The document also summarizes proposed principles from RDA/CODATA on facilitating lawful access to research data while balancing various legal interests through transparent communication of rights.
Plazi or the challenge to free biodiversity data caught in hundreds of millio...agosti
A call for participation of citizen scientists to help to convert the half billion of pages of biodiversity legacy literature into Linked Open Data, an imperative for conservation of the worlds declining biodiversity, but as much as a scientific frontier: How many species are there? Traditionally, citizen scientist plaid a decisive role in describing the Earth's biodiversity. Now the confront a paradoxical challenge that they do not have access to their published scientifc corpus and might have to launch into a second wave of discovery: This time in the printed record.
Lecture held at the "Opportunities and challenges for citizen scientists" workshop at the ETH Zurich, January 23, 2015
This document summarizes a presentation about the Plazi Treatment Repository project. It discusses how Plazi aims to make over 1 million taxonomic treatments openly accessible by semantically enhancing and linking content from biodiversity literature. A major challenge is copyright restrictions on publications, which Plazi addresses by only including non-copyrighted content and material for internal use. The presentation argues for legal changes like mandatory research licenses to further remove barriers to information exchange.
pro-iBiosphere Towards Open Biodiversity Knowledge COOPEUS 2013millerjeremya
The document discusses the goals and approaches of the Pro-iBiosphere project, which aims to make taxonomic data more accessible and interoperable by linking literature to datasets. It outlines challenges around technical and semantic interoperability of taxonomic data. It also describes the prospective approach of extracting structured data from publications and distributing it to biodiversity databases, and the retrospective approach of extracting elements from existing literature to populate databases.
A Step Towards (From) Read to Write Access to Taxonomic Publicationsagosti
Lecture provided at the 8th International Congress of Hymenopterists, Cuzco, Peru, July 23, 2014.
The lectures makes a case to join the bibligraphies and pdf of hymenoptera taxonomy literature on the Biodiersity Literature Repository / Zenodo
Biodiversity informatics involves making biodiversity data accessible through digitization, standardization, and publishing. Biodiversity data is used for taxonomy, biogeography, endangered species monitoring, and more. Key challenges include resolving scientific names and data quality. Major organizations include GBIF, Global Names, and Canadensys which works to mobilize Canadian specimen records. Additional resources can be found through conferences, organizations, and online communities.
Mapping Biodiversity - The Atlas of Living AustraliaDonald Hobern
The document summarizes the Atlas of Living Australia project, which aims to provide open access to biodiversity data. It discusses challenges such as digitizing literature and specimens, standardizing data, integrating taxonomy, and developing tools for users. The Atlas will include a metadata repository, species pages, a regional atlas, and annotation tools to link data and comments. The goal is to make Australia's biological knowledge more accessible and usable.
Bouchout Declaration
Introduction to the Bouchout Declaration for Open Biodiversity Knowledge Management.
The declaration has been initiated by the Pro-iBiosphere consortium and the official launch will be on June 12, 2014 at the Bouchout castle at the Plantentuin Meise, Meise, Belgium.
This presentation has been given at the Swiss "Konservatorentagung 2014, Frauenfeld", May 23.2014
Enhancing the WFO in support of GSPC.pptxWilliam Ulate
This document discusses the World Flora Online (WFO) project, which aims to create an online flora of all known plant species by 2020 in support of the Global Strategy for Plant Conservation. It provides background on previous efforts to comprehensively catalog the world's flora. The WFO will include a taxonomic backbone curated by experts, as well as descriptive content like names, distributions, images and conservation status. It seeks to make plant data more accessible and relevant to users like conservationists. The project supports objectives of the post-2020 global biodiversity framework around improving accessibility and building expert capacity.
The emerging biodiversity data ecosystemCyndy Parr
A talk given at iEvobio11, a conference about Informatics for Phylogenetics, Biodiversity and Evolutionary Biology, held in Norman, Oklahoma June 21-22, 2011
The document discusses the Encyclopedia of Life (EOL) project, which aims to create a web page for every known species containing key information about it. It outlines EOL's goals of aggregating biodiversity data from various sources and making it openly accessible online. The document also describes EOL's efforts to establish a taxonomic framework and infrastructure to facilitate collaborative curation of species pages.
2 Discovery and Acquisition of Data1.pptxvijayapraba1
This document provides an outline of Lecture 2 from the course GEO 802, Data Information Literacy. It discusses various portals and repositories for publishing and finding data, including discipline-specific repositories, as well as directories and indexes of repositories. It also covers data journals and venues for publishing datasets to get them cited. Finally, it lists some exercises for students to find relevant data repositories in their fields and to explore search tools and open data portals.
This document discusses the need for digital curation specialists in library settings to manage the growing volume of scholarly data and output. It recognizes that libraries have the skills and infrastructure to curate digital resources but will need new roles like digital curators, archivists, and data scientists. These roles require new training programs and concentrations in areas like data curation to develop specialists that can preserve, organize, and provide access to digital collections over the long term.
The British Library Datasets Programme aims to:
1) Make research datasets more discoverable, accessible, and reusable by providing persistent identifiers like DOIs.
2) Establish best practices for citing datasets to give their creators proper credit.
3) Develop sustainable models for archiving datasets over the long term through projects with data repositories and publishers.
Global biodiversity data is critical for conservation, policymaking, and scientific research. However, most data is held by small, isolated publishers and is difficult to access. The Global Biodiversity Information Facility (GBIF) aims to mobilize this "small data" by creating common data standards and tools to publish data through its Integrated Publishing Toolkit. This allows data to be discovered through GBIF's portal and used for applications like predicting climate change impacts and invasive species spread. GBIF calls on all data holders to publish their data openly through its framework to build a comprehensive global resource for biodiversity data.
Scott Edmunds: GigaScience - a journal or a database? Lessons learned from th...GigaScience, BGI Hong Kong
Scott Edmunds talk at the HUPO congress in Geneva, September 6th 2011 on GigaScience - a journal or a database? Lessons learned from the Genomics Tsunami.
1. The document describes a semantic network dictionary system for integrating data from various global observation domains like meteorology, agriculture, and remote sensing.
2. The system collects and manages ontological information like terms and definitions from different subject dictionaries and databases.
3. It allows users to browse, visualize relationships between terms, and modify semantic information through an interface connecting various wikis and semantic networks.
1. The document presents a framework for a semantic network dictionary system to integrate data from various disciplines like meteorology, agriculture, and remote sensing for global observation.
2. The system collects and manages ontological information like terms and definitions from existing data dictionaries and thesauri. It registers this information and allows users to browse, modify and visualize the semantic network.
3. The system is meant to help with tasks like metadata design, data integration and knowledge discovery by providing a shared understanding of terms across technical fields. It aims to grow the semantic network over time through continuous registration and editing by experts.
Revolutionizing the Research on Ants through new Methods and Technologies: th...agosti
Invited lecture presented at the XXII Simpósio de Mirmecologia, Ilhéus, BA, Brazil, October 22, 2015. The title takes reference to the ant conference to create a standard protocol to measure and monitor ants - the manual has been published 2000 as "Ants: measuring and monitoring biodiversity" which has been close to 2500 times cited by followup papers - and with the preparation started in 1995 in Ilhéus. The focus is on open access, digital library, sharing of data, publishing and the sociology of myrmecology, and how the data could be used in project like EU-BON.
Plazi's thrive to achive Tim Berners-Lee 5*data for biodiversity literature. Lecture from the Opendata.ch/2015 conference, July1, 2015, Berne, Switzerland http://opendata.ch/projects/opendata-ch2015-konferenz/
This document summarizes the Bouchout Declaration for Open Biodiversity Knowledge Management. The declaration encourages an overarching approach to open biodiversity knowledge management based on principles like open access, open licenses, attribution, infrastructure, registers, persistent identifiers, linked open data, development and business sustainability. It aims to foster free and open access to biodiversity data through policy developments and technical agreements.
This document discusses building an open biodiversity knowledge management system that can extract, store, and serve information on taxa in an interoperable way across kingdoms of life. It notes that the legacy literature contains over 200 million pages but data is incomplete and disconnected. The Pro-iBiosphere project aims to demonstrate how to markup taxon treatments to make them accessible and linkable. Pilots have marked up over 1,500 treatments of plants, fungi, bryophytes, insects and spiders. The document recommends standardizing markup and applying it prospectively to enhance semantic interoperability of biodiversity data.
This document discusses a schema for describing and exchanging the content of taxonomic publications in a way that allows both human and machine access. It proposes using semantic markup like XML to tag elements in publications like names, descriptions, and references in a way that links related data across sources. This would allow content to be more accessible for tasks like data mining while maintaining context. The schema is part of ongoing work by Plazi to apply semantic markup to digitize existing publications and structure new ones for improved dissemination and reuse of taxonomic knowledge.
20110222 behesty monitoring and measuring biodiversityagosti
This document discusses various topics related to monitoring and measuring biodiversity on a global scale. It mentions several key organizations and initiatives, including the Earth Summit, IPBES, NCBI, GBIF, TDWG, and Darwin Core, that are involved with assessing global biodiversity patterns and developing standards for exchanging biodiversity data. The document emphasizes that monitoring biodiversity as a comparative science requires access to data, use of identification aids, metadata standards, networks to share information, and applying data to understand changes over space and time.
The document discusses the future of scientific publishing and open access to scientific literature. It envisions a future where publications are semantically marked up and linked to external data sources to enable advanced text mining and knowledge extraction. Treatments of species would be structured using XML to define content and be linked to identifiers, bibliographic metadata, and other sources. This would allow publications to be queried and analyzed by both humans and machines. Prospective publications could be semantically enhanced from the start, while tools are needed to mark up legacy literature. The goal is open access and dissemination of scientific findings funded by public resources.
The document discusses making taxonomic literature openly accessible in digital format. It proposes marking up publications with XML tags to encode semantic information that allows machines to extract and link data. This would facilitate access to the estimated 100 million pages of existing literature as well as integration of new data. Key recommendations include adopting open access policies, understanding copyright, self-archiving publications, using structured formats like XML, and developing standards and infrastructure to support digitization and interoperability of biodiversity data.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
6. Indicators as powerful widely understood tool
Reed Elsevier, Annual Reports and Financial Statements 2013
http://www.reedelsevier.com/investorcentre/reports%202007/Documents/2013/reed_elsevier_ar_2013.pdf
39% profit
7. Biodiversity research and conservation planning0
Multi-Taxon Specimen Data for Setting Conservation Priorities
Source: Kremen C, et al. 2008. Science 320: 222-226.
Consensus conservation priority areas and
actual and proposed protected areas
2003: Madagascar announces it will triple protected land to 10% coverage
9. EU-Political and Science Decision to support IPBES
EU-BON
European Biodiversity Observation Network
EU-FP7 funded
10. A EU decision in support of environmental policy making
EU-BON
• To build a European Biodiversity Observation
Network
• Measure and predict change over space and time
• Combine Remote Sensing data and on the ground
observation data in predictive modeling
• Tools to inform decision makers (EU-politicians)
11. The basic science question
Hardisty, Nature 502, 171 (2013)
BUT: predictive ecology has substantial data needs
Harfoot, BIH2013, Rome, 2013
What is the future of the biological world?
Imagine if we could:
…Predict community level dynamics of ecosystems at
scales from local to global, based on the ecology and
biology of all individual organisms
13. Communication
EU-BON a child of GEOSS
Global Earth Observation System of Systems
Open Access to remote sensing data from all over the
world
14. The impact of remote sensing data on understanding biodiversity
With sophisticated technologies we can identify different trees in the Amazon…
http://video.ted.com/talk/podcast/2013G/None/GregAsner_2013G-480p.mp4
15. Access to data
…we could create a link to the related data in our biodiversity literature
http://video.ted.com/talk/podcast/2013G/None/GregAsner_2013G-480p.mp4
16. Names as information tags in life sciences
Names
Characteristics
Publications
GenesCollections
Specimens
Distribution
17. Treatments as bits of information
Treatment: sections of publications documenting the
features or distribution of a related group of organisms
(called a “taxon”, plural “taxa”) in ways adhering to highly
formalized conventions. (Catapano, 2010)
Formica obsoleta, Linnaeus 1758: 580
18. Treatments as part of publications
DNA
Specimens Observations
Institution
Pharmacology/epidemiology
Publication
Treatment
Treatment
Treatment
Table
Appendix
Biology/ecology
Reference to other biota
Publication
Treatment
Publication
19. Text
(e.g. PDF)
<tax:treatment>
<tax:nomenclature>
<tax:name>
<tax:xid source="HNS" identifier="193329"/>
<tax:xmldata>
<dc:Genus>Mystrium</dc:Genus>
<dc:Species>leonie</dc:Species>
</tax:xmldata>
Mystrium leonie
</tax:name> Bohn & Verhaagh
<tax:status>n. sp.</tax:status>
Fig 1 D - F
</tax:nomenclature>
<tax:div type="description">
<tax:p>HOLOTYPE WORKER: TL 3.95, HL 1.02, HW 0.
1.30, SI 137, PW 0.73, ML 0.38. Mandible oute
to a sharp apical tooth, the apex parallel to
(Holotype with material in mandibles, so mand
$ described below from paratypes.) Median cly
....
</treatment>
Enhanced and linked text
(XML: Taxonx / Taxpub JATS)
Plazi: Semantic enhanced treatments
20. Automatic extraction and visualization of treatment content
Countries
Madagascar
Anochetus grandidieri Forel
21. Datamining of treatments
Pseudomyrmex ants and Vachellia ant-acacias
are a classic example of mutualism in biology.
allenii
melanoceras
ruddiae
chiapensis
collinsii
cookii
cornigera
globulifera
hindsii
janzenii
mayana
sphaerocephala
boopis
flavicornis
hesperius
ita
janzeni
kuenckeli
mixtecus
nigrocinctus
nigropilosus
opaciceps
particeps
peperi
reconditus
satanicus
simulans
spinicola
subtilissimus
veneficus
ferrugineus
gentlei
gracilis
Transbiotic link network
Associated species linked through
references in taxonomic treatments
Acacia-ant species: Pseudomyrmex gracili
Treatment: original description
Treatment: redescription
Associated ant-acacia: Acacia gentlei
Ants Plants
Photocredits: Alex Wild
Treatment
Treatments linked
through citations
22. The Plazi approach
From treatment
to treatment repository
The Plazi approach
Agosti, D., W. Egloff. 2009. Taxonomic information exchange and copyright: the Plazi approach.
BMC Research Notes 2009, 2:53. doi:10.1186/1756-0500-2-53
24. Analyzing a large corpus of publications: Plazi repository
14,590 specimens
8900 plottable specimens from
1138 unique locations
25. Analyzing a journal: Journal of Hymenoptera Research
5170 specimens
4062 plottable specimens from
1138 unique locations
26. The biodiversity community
Plants
3,400 Herbaria worldwide
10,000 Associate curators and specialists
350,000,000 specimens in collections
180,000,000 specimens digitized
2,000,000,000 specimens including animals
28. The taxonomy publishing world
12,000 Taxonomic Papers on 42,000 Spiders
Since 1757
Publications widely scattered
Source: Jeremy Miller
29. Why is the system broken?
WHY
does it NOTwork?
30. Access to data limited
…we cannotcreate a link to the related biodiversity data
http://video.ted.com/talk/podcast/2013G/None/GregAsner_2013G-480p.mp4
31. Communication
200,000,000+ printed pages
1,900,000 species described
20,000,000+ species treatments
17,000 new species per year
BUT: The data are hidden
Incomplete digitization
Publications are not
semantically enhanced
Collections are incomplete
Data is not linked
Most data are not open
32. Why is the system broken?
Access to a corpus
NOT
single PDF, data point
33. Why is the system broken?
Access to content
NOT
representations
34. Why is the system broken?
Legal issues
Technical issues
Social issues
35. Legal issues: Copyright
Access to ant taxonomic publications through antbase.org /Smithsonian Institution, including currently the entire
body of non-copyrighted publications since 1758 (>4,000 publications or 85,000 pages)
41. Why is the system broken?
WHY
NOT
make it work?
42. European Open Biodiversity Knowledge Management System
European Open
Biodiversity Knowledge
Management System
European Union FP7 funded project
43. European Open Biodiversity Knowledge Management System
Prepare the ground for the creation of
a system for intelligent management
of biodiversity knowledge which will
improve the present system of
taxonomic literature.
44. Legal issues: Copyright: The Blue List
The Blue List
elements of taxonomic information that are not subject to copyright
Patterson, D. J., Egloff, W., Agosti, D., Eades, D., Franz, N., Hagedorn, G., Rees,
J. A. and Remsen, D. P. 2014. Scientific names of organisms: attribution,
rights, and licensing BMC Research Notes 7:79 doi:10.1186/1756-0500-7-79.
45. Legal issues: Copyright: Legal exceptions for research
Legal exceptions for research
Egloff W, Patterson D, Agosti D, Hagedorn G 2014. Open exchange of scientific knowledge and
European copyright: The case of biodiversity information. ZooKeys 414, 109-135. DOI:
10.3897/zookeys.414.7717
48. Technical issues: DOI
Persistent identifiers for data objects and physical objects
Linking data using agreed vocabularies
http://wiki.pro-ibiosphere.eu/wiki/Best_practices_for_stable_URIs
49. Technical issues: DOI
Biodiversity Literature Repository @ Zenodo
public repository for legacy literature using Data Cite DOI
CrossRef to cite (Zenodo) Data Cite DOI?!
50. Technical issues: semantic enhanced publishing
Semantic enhanced publishing
Taxpub JATS
Use DOI as widely as possible
52. Technical issues: semantic publishing
Advanced publishing and dissemination
Form based
Semantnic enhanced TaxPub JATS based publishing
53. Social issues: Bouchout Declaration
http://bouchoutdeclaration.org/ launched June 12, 2014
10 Principles
Free and open use of digital resources
Use of persistent identifiers and linking of data
Policy developments
Developing sustainable business models