Quantifying institutional reach through the human network in natural history collections

Through the Bloodhound proof-of-concept, https://bloodhound-tracker.net an international audience of collectors and determiners of natural history specimens are engaged in the emotive act of claiming their specimens and attributing other specimens to living and deceased mentors and colleagues. Behind the scenes, these claims build links between Open Researcher and Contributor Identifiers (ORCID, https://orcid.org) or Wikidata identifiers for people and Global Biodiversity Information Facility (GBIF) specimen identifiers, predicated by the Darwin Core terms, recordedBy (collected) and identifiedBy (determined). Here we additionally describe the socio-technical challenge in unequivocally resolving people names in legacy specimen data and propose lightweight and reusable solutions. The unique identifiers for the affiliations of active researchers are obtained from ORCID whereas the unique identifiers for institutions where specimens are actively curated are resolved through Wikidata. By constructing closed loops of links between person, specimen, and institution, an interesting suite of potential metrics emerges, all due to the activities of employees and their network of professional relationships. This approach balances a desire for individuals to receive formal recognition for their efforts in natural history collections with that of an institutional-level need to alter budgets in response to easily obtained numeric trends in national and international reach. If handled in a coordinating fashion, this reporting technique may be a significant new driver for specimen digitization efforts on par with Altmetric, https://www.altmetric.com, an important new tool that tracks the impact of publications and delights administrators and authors alike

A botanical demonstration of the potential of linking data using unique identifiers for people

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

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

Data from: Challenges with using names to link digital biodiversity information

The need for a names-based cyber-infrastructure for digital biology is based on the argument that scientific names serve as a standardized metadata system that has been used consistently and near universally for 250 years. As we move towards data-centric biology, name-strings can be called on to discover, index, manage, and analyze accessible digital biodiversity information from multiple sources. Known impediments to the use of scientific names as metadata include synonyms, homonyms, mis-spellings, and the use of other strings as identifiers. We here compare the name-strings in GenBank, Catalogue of Life (CoL), and the Dryad Digital Repository (DRYAD) to assess the effectiveness of the current names-management toolkit developed by Global Names to achieve interoperability among distributed data sources. New tools that have been used here include Parser (to break name-strings into component parts and to promote the use of canonical versions of the names), a modified TaxaMatch fuzzy-matcher (to help manage typographical, transliteration, and OCR errors), and Cross-Mapper (to make comparisons among data sets). The data sources include scientific names at multiple ranks; vernacular (common) names; acronyms; strain identifiers and other surrogates including idiosyncratic abbreviations and concatenations. About 40% of the name-strings in GenBank are scientific names representing about 400,000 species or infraspecies and their synonyms. Of the formally-named terminal taxa (species and lower taxa) represented, about 82% have a match in CoL. Using a subset of content in DRYAD, about 45% of the identifiers are names of species and infraspecies, and of these only about a third have a match in CoL. With simple processing, the extent of matching between DRYAD and CoL can be improved to over 90%. The findings confirm the necessity for name-processing tools and the value of scientific names as a mechanism to interconnect distributed data, and identify specific areas of improvement for taxonomic data sources. Some areas of diversity (bacteria and viruses) are not well represented by conventional scientific names, and they and other forms of strings (acronyms, identifiers, and other surrogates) that are used instead of names need to be managed in reconciliation services (mapping alternative name-strings for the same taxon together). On-line resolution services will bring older scientific names up to date or convert surrogate name-strings to scientific names should such names exist. Examples are given of many of the aberrant forms of ‘names’ that make their way into these databases. The occurrence of scientific names with incorrect authors, such as chresonyms within synonymy lists, is a quality-control issue in need of attention. We propose a future-proofing solution that will empower stakeholders to take advantage of the name-based infrastructure at little cost. This proposed infrastructure includes a standardized system that adopts or creates UUIDs for name-strings, software that can identify name-strings in sources and apply the UUIDs, reconciliation and resolution services to manage the name-strings, and an annotation environment for quality control by users of name-strings

Data from: Challenges with using names to link digital biodiversity information

The need for a names-based cyber-infrastructure for digital biology is based on the argument that scientific names serve as a standardized metadata system that has been used consistently and near universally for 250 years. As we move towards data-centric biology, name-strings can be called on to discover, index, manage, and analyze accessible digital biodiversity information from multiple sources. Known impediments to the use of scientific names as metadata include synonyms, homonyms, mis-spellings, and the use of other strings as identifiers. We here compare the name-strings in GenBank, Catalogue of Life (CoL), and the Dryad Digital Repository (DRYAD) to assess the effectiveness of the current names-management toolkit developed by Global Names to achieve interoperability among distributed data sources. New tools that have been used here include Parser (to break name-strings into component parts and to promote the use of canonical versions of the names), a modified TaxaMatch fuzzy-matcher (to help manage typographical, transliteration, and OCR errors), and Cross-Mapper (to make comparisons among data sets). The data sources include scientific names at multiple ranks; vernacular (common) names; acronyms; strain identifiers and other surrogates including idiosyncratic abbreviations and concatenations. About 40% of the name-strings in GenBank are scientific names representing about 400,000 species or infraspecies and their synonyms. Of the formally-named terminal taxa (species and lower taxa) represented, about 82% have a match in CoL. Using a subset of content in DRYAD, about 45% of the identifiers are names of species and infraspecies, and of these only about a third have a match in CoL. With simple processing, the extent of matching between DRYAD and CoL can be improved to over 90%. The findings confirm the necessity for name-processing tools and the value of scientific names as a mechanism to interconnect distributed data, and identify specific areas of improvement for taxonomic data sources. Some areas of diversity (bacteria and viruses) are not well represented by conventional scientific names, and they and other forms of strings (acronyms, identifiers, and other surrogates) that are used instead of names need to be managed in reconciliation services (mapping alternative name-strings for the same taxon together). On-line resolution services will bring older scientific names up to date or convert surrogate name-strings to scientific names should such names exist. Examples are given of many of the aberrant forms of ‘names’ that make their way into these databases. The occurrence of scientific names with incorrect authors, such as chresonyms within synonymy lists, is a quality-control issue in need of attention. We propose a future-proofing solution that will empower stakeholders to take advantage of the name-based infrastructure at little cost. This proposed infrastructure includes a standardized system that adopts or creates UUIDs for name-strings, software that can identify name-strings in sources and apply the UUIDs, reconciliation and resolution services to manage the name-strings, and an annotation environment for quality control by users of name-strings

The 'making of' the Mulligans Flat - Goorooyarroo experimental restoration project

What happens when park managers and ecological researchers join forces to build an evidence-based approach to restoring a nature reserve? This project shows how a spirit of cooperation and inventiveness overcome a range of challenges at one of the National Capital region's most valuable examples of critically endangered box-gum grassy woodland

A Proposed Metadata Standard for Recording and Sharing Attribution Information in Biodiversity

Research collections are an important tool for understanding the Earth, its systems, and human interaction. Despite the importance of collections, many are not maintained or curated as thoroughly as we would like. Part of the reason for this is the lack of professional reward for collection, curation, or maintenance. To address this gap in attribution metadata, the Research Data Alliance (RDA) and the Biodiversity Information Standards (TDWG) organization co-endorsed a Working Group to create recommendations for the representation of attribution metadata. After 18 months, this Working Group recommended a very simple data exchange standard to link people, the curatorial actions they perform, and the digital or physical objects they are curating. These recommendations are discussed in the context of community-developed use cases. Future work includes: exploration of a Darwin Core extension, best practices on how to best adopt these recommendations, and possible solutions to help accelerate the process of connecting people and their activities in legacy and future data. To explore options for making collections work more visible and citable, we tested the use of digital annotation tools and person identifiers in curation workflows.  The results from this pilot project in collaboration with ORCID and Data Futures to display specimens on an ORCID profile will be presented

Association between apolipoprotein E epsilon 4 and neuropsychiatric symptoms during interferon alpha treatment for chronic hepatitis C

Neuropsychiatric complications are common in patients with chronic hepatitis C undergoing treatment with interferon alpha. These side effects include alterations of mood, cognition, and neuroendocrine function and are unpredictable. In a number of neurological disorders characterized by neuropsychiatric symptoms and cognitive dysfunction, inheritance of an apolipoprotein E (APOE) epsilon4 allele is associated with adverse neuropsychiatric outcomes. The authors present evidence that the APOE genotype may influence a patient's neuropsychiatric response to interferon alpha treatment. The inheritance of APOE genotypes was examined in 110 patients with chronic hepatitis C treated with interferon alpha. A retrospective investigation was conducted by assessing the rates of psychiatric referral and neuropsychiatric symptoms experienced during treatment along with other complaints indicating psychological distress. A highly statistically significant association was seen between APOE genotypes and interferon-induced neuropsychiatric symptoms. Patients with an epsilon4 allele were more likely to be referred to a psychiatrist and had more neuropsychiatric symptoms during antiviral treatment than those without an epsilon4 allele. Additionally, patients with an epsilon4 allele were more likely to experience irritability or anger and anxiety or other mood symptoms. These data demonstrate that an individual's APOE genotype may influence the neuropsychiatric response to antiviral therapy with interferon alpha. Prospective studies evaluating the importance of APOE in susceptibility to interferon alpha-induced neuropsychiatric complications are needed. Moreover, pathways involving APOE should be considered in understanding the pathophysiology of interferon alpha-induced neuropsychiatric complications