Do giant barnacles contribute to deep-water biogenic reef formation in Maltese waters?

Deep-sea ROV surveys in the west Malta Graben allowed re-evaluation of previous work on the association of the giant barnacle, Pachylasma giganteum, with cold-water corals and other habitat-forming species, and this species’ contribution to formation of biogenic structures. While only a minor contributor to habitat architecture when anthozoans and other large sessile species are dominant, P. giganteum may become a habitat-former in the absence of competing species.peer-reviewe

Bioschemas:schema.org for the Life Sciences

Websites are commonly used to expose data to end users, enabling search, filter, and download capabilities making it easier for users to find, organize and obtain data relevant to their own interests. With the continuous growth of data in the Life Sciences domain, it becomes difficult for users to easily find information required for their research on one single website. Search engines should make it easier for researchers to search and retrieve collated information from multiple sites so they can better decide where to go next. Schema.org is a collaborative project providing schemas for semantically structuring data in web pages. By adding semantic mark-up it becomes easier to determine whether a web page refers to a book or a movie. It also facilitates summarizing information in a fashion similar to infoboxes used in Wikipedia. Bioschemas is a community effort aiming to extend schema.org to support mark-up for Life Sciences websites. Here we present an overview of the main types used and proposed by Bioschemas in order to support such mark up

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

BACKGROUND: Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. RESULTS: We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. Availability: (interactive), (download). CONCLUSION: From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous analytical tools

Overview of LiLAS 2020 -- Living Labs for Academic Search

Academic Search is a timeless challenge that the field of Information Retrieval has been dealing with for many years. Even today, the search for academic material is a broad field of research that recently started working on problems like the COVID-19 pandemic. However, test collections and specialized data sets like CORD-19 only allow for system-oriented experiments, while the evaluation of algorithms in real-world environments is only available to researchers from industry. In LiLAS, we open up two academic search platforms to allow participating research to evaluate their systems in a Docker-based research environment. This overview paper describes the motivation, infrastructure, and two systems LIVIVO and GESIS Search that are part of this CLEF lab.Comment: Manuscript version of the CLEF 2020 proceedings pape

In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central

Motivation Although full-text articles are provided by the publishers in electronic formats, it remains a challenge to find related work beyond the title and abstract context. Identifying related articles based on their abstract is indeed a good starting point; this process is straightforward and does not consume as many resources as full-text based similarity would require. However, further analyses may require in-depth understanding of the full content. Two articles with highly related abstracts can be substantially different regarding the full content. How similarity differs when considering title-and-abstract versus full-text and which semantic similarity metric provides better results when dealing with full-text articles are the main issues addressed in this manuscript. Methods We have benchmarked three similarity metrics – BM25, PMRA, and Cosine, in order to determine which one performs best when using concept-based annotations on full-text documents. We also evaluated variations in similarity values based on title-and-abstract against those relying on full-text. Our test dataset comprises the Genomics track article collection from the 2005 Text Retrieval Conference. Initially, we used an entity recognition software to semantically annotate titles and abstracts as well as full-text with concepts defined in the Unified Medical Language System (UMLS®). For each article, we created a document profile, i.e., a set of identified concepts, term frequency, and inverse document frequency; we then applied various similarity metrics to those document profiles. We considered correlation, precision, recall, and F1 in order to determine which similarity metric performs best with concept-based annotations. For those full-text articles available in PubMed Central Open Access (PMC-OA), we also performed dispersion analyses in order to understand how similarity varies when considering full-text articles. Results We have found that the PubMed Related Articles similarity metric is the most suitable for full-text articles annotated with UMLS concepts. For similarity values above 0.8, all metrics exhibited an F1 around 0.2 and a recall around 0.1; BM25 showed the highest precision close to 1; in all cases the concept-based metrics performed better than the word-stem-based one. Our experiments show that similarity values vary when considering only title-and-abstract versus full-text similarity. Therefore, analyses based on full-text become useful when a given research requires going beyond title and abstract, particularly regarding connectivity across articles. Availability Visualization available at ljgarcia.github.io/semsim.benchmark/, data available at http://dx.doi.org/10.5281/zenodo.13323.The authors acknowledge the support from the members of Temporal Knowledge Bases Group at Universitat Jaume I. Funding: LJGC and AGC are both self-funded, RB is funded by the “Ministerio de Economía y Competitividad” with contract number TIN2011-24147

Bioinformatic workflows : G-PIPE as an implementation

We present G-PIPE, a graphic pipeline generator for PISE that allows the definition of pipelines, parameterization of its component methods, and storage of metadata in XML formats. Our implementation goes beyond macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. We also discuss the role of ontologies as as guidance systems in order to provide users with the possibility to define abstract work-flows, and execute them. A relevant baseline ontology is presented. Availability: http://if-web.imb.uq.edu.a

Refining deep-sea habitat classification schemes based on recent surveys in Maltese waters

ROV imagery is leading to the discovery of diverse deep-sea habitat types in the Malta Fisheries Management Zone (FMZ) at depths of 200 to 1000 meters. These include rocky bottoms with mixed assemblages dominated by cold-water corals and gorgonians, as well as sponges with both encrusting and erect growth habits. Vast expanses of different types of soft-bottom habitats are also present, mostly dominated by Anthozoa, Foraminifera and/or burrowing infauna. New habitat categories will need to be added to the existing habitat classification schemes for the deep Mediterranean Sea, including those of the European Nature Information System (EUNIS), and the Regional Activity Centre for Specially Protected Areas (RAC/SPA), to accommodate some of these discoveries.peer-reviewe

An open annotation ontology for science on web 3.0

Background: There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Methods: Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. Results: This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables "stand-off" or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO's Google Code page: http://code.google.com/p/annotation-ontology/. Conclusions: The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors

New depth record of the precious red coral Corallium rubrum for the Mediterranean

Live colonies of the precious red coral Corallium rubrum have previously been recorded at depths of 600 -800 m in the Sicily Channel, but deep -water populations of this species remain poorly known. During a recent research expedition within the 25 nautical mile Fisheries Management Zone around the Maltese Islands, numerous colonies growing deeper than 800 m, down to depths of 1016 m were observed. These colonies were part of a diverse community of habitat -forming species of scleractinians, gorgonians and antipatharians.peer-reviewe

On the occurrence of Coronaster briareus (Echinodermata, Forcipulatida, Asteriidae) in the Mediterranean Sea

The sea star Coronaster briareus (Verrill Am J Sci (Ser III), 1882) is reported for the first time from the Mediterranean Sea. A total of 26 individuals were sighted in Maltese waters during ROV surveys made in July 2015 and June–July 2016. The identity of the species was confirmed through morphological examination of a specimen collected in June 2016. This identification is discussed in the light of inconsistencies in the published descriptions of species of Coronaster recorded from the Atlantic, and of individuals belonging to this genus recorded from the eastern Atlantic and whose coloration does not match that of C. briareus or C. volsellatus (the only species of Coronaster hitherto known from the Atlantic). The presence of numerous individuals of C. briareus in Maltese waters, recorded on two occasions a year apart over a relatively large area, indicates that there is an established population. This represents a considerable expansion of the distribution range of this species, which is mostly known from the western Atlantic. Possible reasons for its presence in Maltese waters are discussed, but the dynamics of the occurrence of C. briareus in the central Mediterranean remain unknown.peer-reviewe