The Trouble with Triplets in Biodiversity Informatics: A Data-Driven Case against Current Identifier Practices

The biodiversity informatics community has discussed aspirations and approaches for assigning globally unique identifiers (GUIDs) to biocollections for nearly a decade. During that time, and despite misgivings, the de facto standard identifier has become the “Darwin Core Triplet”, which is a concatenation of values for institution code, collection code, and catalog number associated with biocollections material. Our aim is not to rehash the challenging discussions regarding which GUID system in theory best supports the biodiversity informatics use case of discovering and linking digital data across the Internet, but how well we can link those data together at this moment, utilizing the current identifier schemes that have already been deployed. We gathered Darwin Core Triplets from a subset of VertNet records, along with vertebrate records from GenBank and the Barcode of Life Data System, in order to determine how Darwin Core Triplets are deployed “in the wild”. We asked if those triplets follow the recommended structure and whether they provide an easy and unambiguous means to track from specimen records to genetic sequence records. We show that Darwin Core Triplets are often riddled with semantic and syntactic errors when deployed and curated in practice, despite specifications about how to construct them. Our results strongly suggest that Darwin Core Triplets that have not been carefully curated are not currently serving a useful role for relinking data. We briefly consider needed next steps to overcome current limitations.     

Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers

Given the growing wealth of downstream information, the integration of molecular and non-molecular data on a given organism has become a major challenge. For micro-organisms, this information now includes a growing collection of sequenced genes and complete genomes, and for communities of organisms it includes metagenomes. Integration of the data is facilitated by the existence of authoritative, community-recognized, consensus identifiers that may form the heart of so-called information knuckles. The Genomic Standards Consortium (GSC) is building a mapping of identifiers across a group of federated databases with the aim to improve navigation across these resources and to enable the integration of their information in the near future. In particular, this is possible because of the existence of INSDC Genome Project Identifiers (GPIDs) and accession numbers, and the ability of the community to define new consensus identifiers such as the culture identifiers used in the StrainInfo.net bioportal. Here we outline (1) the general design of the Genomic Rosetta Stone project, (2) introduce example linkages between key databases (that cover information about genomes, 16S rRNA gene sequences, and microbial biological resource centers), and (3) make an open call for participation in this project providing a vision for its future use.     

LSID Tester,a tool for testing Life Science Identifier resolution services

Background  

Life Science Identifiers (LSIDs) are persistent, globally unique identifiers for biological objects. The decentralised nature of LSIDs makes them attractive for identifying distributed resources. Data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) are distributed over many different providers, and this community has adopted LSIDs as the identifier of choice.     

Biodiversity informatics: the challenge of linking data and the role of shared identifiers

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers [such as Digital Object Identifiers (DOIs) and Life Science Identifiers (LSIDs)], and the implementation of services that link those identifiers.     

MatchMiner: a tool for batch navigation among gene and gene product identifiers

MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic' research. The user inputs a list of gene identifiers and then uses the Merge function to find the overlap with a second list of identifiers of either the same or a different type or uses the LookUp function to find corresponding identifiers.     

Linking aboveground and belowground diversity

Aboveground and belowground species interactions drive ecosystem properties at the local scale, but it is unclear how these relationships scale-up to regional and global scales. Here, we discuss our current knowledge of aboveground and belowground diversity links from a global to a local scale. Global diversity peaks towards the Equator for large, aboveground organisms, but not for small (mainly belowground) organisms, suggesting that there are size-related biodiversity gradients in global aboveground-belowground linkages. The generalization of aboveground-belowground diversity relationships, and their role in ecosystem functioning, requires surveys at scales that are relevant to the organisms and ecosystem properties. Habitat sizes and diversity gradients can differ significantly between aboveground and belowground organisms and between ecosystems. These gradients in biodiversity and plant community trait perception need to be acknowledged when studying aboveground-belowground biodiversity linkages.     

Habitat monitoring in Europe: a description of current practices

Monitoring of biodiversity at the level of habitats is becoming increasingly common. Here we describe current practices in habitat monitoring based on 150 schemes in Europe. Most schemes were initiated after 1990 in response to EU nature directives or habitat management/restoration actions, with funding mostly from European or national sources. Schemes usually monitor both the spatial distribution and the quality of the habitats, and they frequently collect data on environmental parameters and potential causes of changes. Many schemes are local or regional rather than national or international in scope, and sampling effort varies greatly across spatial and temporal scales. Experimental design is used in half of the schemes, however, data are rarely analysed by advanced statistics. Most schemes require two months or less per year in manpower and are typically run by professionals rather than by volunteers. Estimated salaries plus equipment costs average 650,000 Euro per year per scheme, and add up to 80 million Euros annually. Costs are particularly high for schemes based on European or international law and for schemes funded by European or national sources. Costs are also high in schemes in which sampling sites are selected subjectively rather than based on sampling theory, and in schemes that do not use field mapping or remote sensing to document spatial variation in habitats. Our survey demonstrates promising developments in European habitat monitoring but also underlines the need for better spatial coverage, documentation of spatial variaton, improved sampling design and advanced data analysis. Such improvements are essential if we are to judge progress towards the 2010 biodiversity targets.     

Ten simple rules for making a vocabulary FAIR

We present ten simple rules that support converting a legacy vocabulary—a list of terms available in a print-based glossary or in a table not accessible using web standards—into a FAIR vocabulary. Various pathways may be followed to publish the FAIR vocabulary, but we emphasise particularly the goal of providing a globally unique resolvable identifier for each term or concept. A standard representation of the concept should be returned when the individual web identifier is resolved, using SKOS or OWL serialised in an RDF-based representation for machine-interchange and in a web-page for human consumption. Guidelines for vocabulary and term metadata are provided, as well as development and maintenance considerations. The rules are arranged as a stepwise recipe for creating a FAIR vocabulary based on the legacy vocabulary. By following these rules you can achieve the outcome of converting a legacy vocabulary into a standalone FAIR vocabulary, which can be used for unambiguous data annotation. In turn, this increases data interoperability and enables data integration.     

Indifferent Philosophy versus Almighty Authority: On consistency,consensus and unitary taxonomy

The ability of the taxonomic community to heed Charles Godfray's wake‐up call to create ‘unitary’ taxonomic systems and make them available on the internet is hampered by real difficulties over achieving taxonomic consistency, and a cultural reluctance amongst systematists to embrace consensus. This paper explores these issues by examining the taxonomic history of an African milkweed butterfly, Amauris damocles sensu lato. Recent differences of opinion over the classification of this insect relate to fundamental differences in the theory and practice of systematics, from creationism through authoritarianism to cladistics, differences of a kind that will forever bedevil the distributed taxonomic system. If practical unitary schemes are to emerge, then the taxonomic community will need to adopt new ways of managing and recording taxonomic change, and develop a more responsible attitude towards the needs of others who are dependent of the primary products of systematics ‐names, and the classification schemes they symbolize.     

Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data

In proteomics, protein identifications are reported and stored using an unstable reference system: protein identifiers. These proprietary identifiers are created individually by every protein database and can change or may even be deleted over time. To estimate the effect of the searched protein sequence database on the long-term storage of proteomics data we analyzed the changes of reported protein identifiers from all public experiments in the Proteomics Identifications (PRIDE) database by November 2010. To map the submitted protein identifier to a currently active entry, two distinct approaches were used. The first approach used the Protein Identifier Cross Referencing (PICR) service at the EBI, which maps protein identifiers based on 100% sequence identity. The second one (called logical mapping algorithm) accessed the source databases and retrieved the current status of the reported identifier. Our analysis showed the differences between the main protein databases (International Protein Index (IPI), UniProt Knowledgebase (UniProtKB), National Center for Biotechnological Information nr database (NCBI nr), and Ensembl) in respect to identifier stability. For example, whereas 20% of submitted IPI entries were deleted after two years, virtually all UniProtKB entries remained either active or replaced. Furthermore, the two mapping algorithms produced markedly different results. For example, the PICR service reported 10% more IPI entries deleted compared with the logical mapping algorithm. We found several cases where experiments contained more than 10% deleted identifiers already at the time of publication. We also assessed the proportion of peptide identifications in these data sets that still fitted the originally identified protein sequences. Finally, we performed the same overall analysis on all records from IPI, Ensembl, and UniProtKB: two releases per year were used, from 2005. This analysis showed for the first time the true effect of changing protein identifiers on proteomics data. Based on these findings, UniProtKB seems the best database for applications that rely on the long-term storage of proteomics data.     

A comprehensive dictionary of protein accession codes for complete protein accession identifier alias resolving

In mass spectrometry-based proteomics, protein identification results usually consist of peptide sequences and database-dependent accession identifiers of the matching proteins. Often certain annotations are only available in particular databases that in turn must be queried by a certain identifier. In order to simplify and unify the tracing of identified proteins back to their original annotation information, a system capable of set-oriented mapping the different accession identifiers of proteins derived from multiple sequence database sources has been developed. This allows unification of the access to protein information and tracing to other online resources providing additional information as well as resolving cross-references of protein identifications. The interface of seqDB is available via http://www.protein-ms.de following the link to seqDB.     

Zimbabwe's wildlife conservation regime: Rural farmers and the state

This article examines the rhino and elephant conservation policies of Zimbabwe, focusing on the historical experiences of rural farmers with colonial and post-colonial wildlife policies. It begins by defining the social and political ramifications of the current environmental conservation debate in Africa, and how these are crucially affected by rural people's perceptions of environmental goods. Next, the paper explores the exploitative colonial legacy of wildlife conservation in Zimbabwe, and how that legacy has or has not been transformed since independence. The paper pays close attention to the development of linkages between rural farmers, local conservation NGOs, and local and national governmental bodies. Finally, the paper finds that, while many positive linkages have been made between conservation authorities and rural farmers and ranchers in elephant conservation programs, few such linkages have been made in the various rhino conservation schemes. Since Zimbabwe has been relatively successful in conserving its elephant population, but relatively unsuccessful in stopping rhino poaching, the paper concludes that the development of positive linkages between rural farmers and the state, which include heavy doses of popular participation at the grassroots level, is crucial for any successful natural resource policy.     

Towards a collaborative, global infrastructure for biodiversity assessment

Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform today's portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge.     

Attitudes toward Post‐Trial Access to Medical Interventions: A Review of Academic Literature,Legislation, and International Guidelines

There is currently no international consensus around post‐trial obligations toward research participants, community members, and host countries. This literature review investigates arguments and attitudes toward post‐trial access. The literature review found that academic discussions focused on the rights of research participants, but offered few practical recommendations for addressing or improving current practices. Similarly, there are few regulations or legislation pertaining to post‐trial access. If regulatory changes are necessary, we need to understand the current arguments, legislation, and attitudes towards post‐trial access and participants and community members. Given that clinical trials conducted in low‐income countries will likely continue, there is an urgent need for consideration of post‐trial benefits for participants, communities, and citizens of host countries. While this issue may not be as pressing in countries where participants have access to healthcare and medicines through public schemes, it is particularly important in regions where this may not be available.     

Functional traits as indicators of biodiversity response to land use changes across ecosystems and organisms

Rigorous and widely applicable indicators of biodiversity are needed to monitor the responses of ecosystems to global change and design effective conservation schemes. Among the potential indicators of biodiversity, those based on the functional traits of species and communities are interesting because they can be generalized to similar habitats and can be assessed by relatively rapid field assessment across eco-regions. Functional traits, however, have as yet been rarely considered in current common monitoring schemes. Moreover, standardized procedures of trait measurement and analyses have almost exclusively been developed for plants but different approaches have been used for different groups of organisms. Here we review approaches using functional traits as biodiversity indicators focussing not on plants as usual but particularly on animal groups that are commonly considered in different biodiversity monitoring schemes (benthic invertebrates, collembolans, above ground insects and birds). Further, we introduce a new framework based on functional traits indices and illustrate it using case studies where the traits of these organisms can help monitoring the response of biodiversity to different land use change drivers. We propose and test standard procedures to integrate different components of functional traits into biodiversity monitoring schemes across trophic levels and disciplines. We suggest that the development of indicators using functional traits could complement, rather than replace, the existent biodiversity monitoring. In this way, the comparison of the effect of land use changes on biodiversity is facilitated and is expected to positively influence conservation management practices.     

Revegetation rewilds the soil bacterial microbiome of an old field

Ecological restoration is a globally important and well‐financed management intervention used to combat biodiversity declines and land degradation. Most restoration aims to increase biodiversity towards a reference state, but there are concerns that intended outcomes are not reached due to unsuccessful interventions and land‐use legacy issues. Monitoring biodiversity recovery is essential to measure success; however, most projects remain insufficiently monitored. Current field‐based methods are hard to standardize and are limited in their ability to assess important components of ecosystems, such as bacteria. High‐throughput amplicon sequencing of environmental DNA (metabarcoding of eDNA) has been proposed as a cost‐effective, scalable and uniform ecological monitoring solution, but its application in restoration remains largely untested. Here we show that metabarcoding of soil eDNA is effective at demonstrating the return of the native bacterial community in an old field following native plant revegetation. Bacterial composition shifted significantly after 8 years of revegetation, where younger sites were more similar to cleared sites and older sites were more similar to remnant stands. Revegetation of the native plant community strongly impacted on the belowground bacterial community, despite the revegetated sites having a long and dramatically altered land‐use history (i.e. >100 years grazing). We demonstrate that metabarcoding of eDNA provides an effective way of monitoring changes in bacterial communities that would otherwise go unchecked with conventional monitoring of restoration projects. With further development, awareness of microbial diversity in restoration has significant scope for improving the efficacy of restoration interventions more broadly.