Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies

Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent "parts", but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies---structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here we assess whether the proximity of ontology-annotated characters within an ontology predicts evolutionary patterns. To do so, we measure phylogenetic information across characters and evaluate if it is hierarchically structured by ontological knowledge---in much the same way as phylogeny structures across-species diversity. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to datasets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially structured by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to addressing particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that ontology does indeed structure phylogenetic information, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological datasets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may structure it: phylogeny, development, or convergence.

Translating TDWG Controlled Vocabularies

Users may be more likely to understand and utilize standards if they are able to read labels and definitions of terms in their own languages. Increasing standards usage in non-English speaking parts of the world will be important for making biodiversity data from across the globe more uniformly available. For these reasons, it is important for Biodiversity Information Standards (TDWG) to make its standards widely available in as many languages as possible. Currently, TDWG has six ratified controlled vocabularies*1, 2, 3, 4, 5, 6 that were originally available only in English. As an outcome of this workshop, we have made term labels and definitions in those vocabularies available in the languages of translators who participated in its sessions. In the introduction, we reviewed the concept of vocabularies, explained the distinction between term labels and controlled value strings, and described how multilingual labels and definitions fit into the standards development process. The introduction was followed by working sessions in which individual translators or small groups working in a single language filled out Google Sheets with their translations. The resulting translations were compiled along with attribution information for the translators and made freely available in JavaScript Object Notation (JSON) and comma separated values (CSV) formats.*7

RS-ADR: A Reference Standard for Adverse Drug Reaction Signal Assessment by Integrating Real-World Evidence and Controlled Vocabularies (Preprint)

BACKGROUND Pharmacovigilance using real-world data (RWD), such as multicenter electronic health records (EHRs), yields massively parallel adverse drug reaction (ADR) signals. However, proper validation of computationally detected ADR signals is not possible due to the lack of a reference standard for positive and negative associations. OBJECTIVE To develop a reference standard for ADR (RS-ADR) to streamline the systematic detection, assessment, and understanding of almost all drug-ADR associations suggested by RWD analyses. METHODS We integrated well-known reference sets for drug-ADR pairs, including Side Effect Resource (SIDER), Observational Medical Outcomes Partnership, and EU-ADR. We created a pharmacovigilance dictionary using controlled vocabularies and systematically annotated EHR data. Drug-ADR associations computed from MetaLAB and MetaNurse analyses of multicenter EHRs and extracted from the FDA Adverse Event Reporting System (FAERS) were integrated as ‘empirically determined’ positive and negative reference sets by means of cross-validation between institutions. RESULTS The RS-ADR consisted of 1,344 drugs, 4,485 ADRs, and 6,027,840 drug-ADR pairs with positive and negative consensus votes as pharmacovigilance reference sets. After curation of the initial version of RS-ADR, novel ADR signals such as ‘famotidine’-‘hepatic function abnormal’ were detected and reasonably validated by RS-ADR. While the validation of the entire reference standard is challenging, especially with this initial version, the reference standard will improve as more RWD participate in the consensus voting with advanced pharmacovigilance dictionaries and analytic algorithms. One can check if a drug-ADR pair has been reported by our web-based search interface for RS-ADRs available at https://bioemr2.snubi.org:19108/. CONCLUSIONS RS-ADRs enriched with the pharmacovigilance dictionary, ADR knowledge, and real-world evidence from EHRs may streamline the systematic detection, evaluation, and causality assessment of computationally detected ADR signals.

Organizing subject access to cultural heritage in Swedish online museums

PurposeThe study aims to paint a representative picture of the current state of search interfaces of Swedish online museum collections, focussing on search functionalities with particular reference to subject searching, as well as the use of controlled vocabularies, with the purpose of identifying which improvements of the search interfaces are needed to ensure high-quality information retrieval for the end user.Design/methodology/approachIn the first step, a set of 21 search interface criteria was identified, based on related research and current standards in the domain of cultural heritage knowledge organization. Secondly, a complete set of Swedish museums that provide online access to their collections was identified, comprising nine cross-search services and 91 individual museums' websites. These 100 websites were each evaluated against the 21 criteria, between 1 July and 31 August 2020.FindingsAlthough many standards and guidelines are in place to ensure quality-controlled subject indexing, which in turn support information retrieval of relevant resources (as individual or full search results), the study shows that they are not broadly implemented, resulting in information retrieval failures for the end user. The study also demonstrates a strong need for the implementation of controlled vocabularies in these museums.Originality/valueThis study is a rare piece of research which examines subject searching in online museums; the 21 search criteria and their use in the analysis of the complete set of online collections of a country represents a considerable and unique contribution to the fields of knowledge organization and information retrieval of cultural heritage. Its particular value lies in showing how the needs of end users, many of which are documented and reflected in international standards and guidelines, should be taken into account in designing search tools for these museums; especially so in subject searching, which is the most complex and yet the most common type of search. Much effort has been invested into digitizing cultural heritage collections, but access to them is hindered by poor search functionality. This study identifies which are the most important aspects to improve.

Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis

To identify sequences with a role in microbial pathogenesis, we assessed the adequacy of their annotation by existing controlled vocabularies and sequence databases. Our goal was to regularize descriptions of microbial pathogenesis for improved integration with bioinformatic applications. Here we review the challenges of annotating sequences for pathogenic activity. We relate the categorization of more than 2750 sequences of pathogenic microbes through a controlled vocabulary called Functions of Sequences of Concern (FunSoCs). These allow for an ease of description by both humans and machines. We provide a subset of 220 fully annotated sequences in the supplementary material as examples. The use of this compact (∼30 terms) controlled vocabulary has potential benefits for research in microbial genomics, public health, biosecurity, biosurveillance, and the characterization of new and emerging pathogens.

Speaking the Same Language: Using Controlled Vocabularies to Search Museum Collections Databases

<p>This study set out to see how controlled vocabularies help people find collections materials in electronic museum databases.It did this by interviewing collections staff from four museums. Eight people from library and non-library work areas at the four museums, who regularly search a museum database in the course of their work, were asked about their experiences with using controlled vocabularies to search. How people used controlled terms depended upon their job tasks and upon their knowledge of terms, past experience and training, and whether they trusted that terms would deliver good search results. Difficulties in using them were identified as being to do with terms themselves; the knowledge of the person searching; and the quality of information in the database. Despite controlled terms rarely being used alone for searching, respondents considered that controlled terminologies are important tools within museum databases for accessing collections. Controlled terms are resource intensive and need institutional backing to work well. Peer support, formal training, staff with database and controlled terms experience, and access to terms lists are some specific factors that would assist controlled vocabularies to work better for the people who search museum databases. Museums need to allocate sufficient financial and administrative resources to controlled terms, if they are serious about improving access to their collections.</p>

Speaking the Same Language: Using Controlled Vocabularies to Search Museum Collections Databases

<p>This study set out to see how controlled vocabularies help people find collections materials in electronic museum databases.It did this by interviewing collections staff from four museums. Eight people from library and non-library work areas at the four museums, who regularly search a museum database in the course of their work, were asked about their experiences with using controlled vocabularies to search. How people used controlled terms depended upon their job tasks and upon their knowledge of terms, past experience and training, and whether they trusted that terms would deliver good search results. Difficulties in using them were identified as being to do with terms themselves; the knowledge of the person searching; and the quality of information in the database. Despite controlled terms rarely being used alone for searching, respondents considered that controlled terminologies are important tools within museum databases for accessing collections. Controlled terms are resource intensive and need institutional backing to work well. Peer support, formal training, staff with database and controlled terms experience, and access to terms lists are some specific factors that would assist controlled vocabularies to work better for the people who search museum databases. Museums need to allocate sufficient financial and administrative resources to controlled terms, if they are serious about improving access to their collections.</p>

Vocabulary Control in Nautical Information Resources

Nautical charts are an essential information resource for safe navigation. However, they are not only a useful resource for navigators; According to the International Hydrological Organization (IHO), they essentially fulfill two functions: 1) Maritime navigation, since most hydrographic services have the obligation to provide coverage of the nautical charts of their national waters, in all coastal waters, including major ports and smaller marinas of purely local interest. and 2) as a source of information, since national nautical charts present a detailed configuration of the seabed. Information on the shape of the seabed is required by a diversity of users in addition to navigators; for example, engineers interested in onshore construction, dredging contractors, oceanographers, defense agencies, coastal zone managers, etc. Traditionally, there are three essential elements that play an important role in information retrieval: title, author, and subject access point. Among the latter, one can distinguish indexing by natural language and by controlled vocabularies. The thematic access points, makes it easier for the user to search and retrieve all types of resources that satisfy their information needs. Traditionally in the processing of nautical charts the natural language is used predominantly, motivated by a lack of availability of a controlled vocabulary specific to the área in Spanish. The objective of this work is aimed at establishing the criteria for the construction of a controlled vocabulary in Spanish in the field of nautical charts.

Data Reference Syntax (DRS) for bias-adjusted CMIP6 simulations

This document specifies the Data Reference Syntax (DRS) elements for managing bias-adjusted CMIP6 simulation data. The document includes file naming conventions and metadata as NetCDF attributes. The DRS elements are allowed to either assume values defined by Controlled Vocabularies (CV), or free text, or free text with build rules.