A Workflow for the Semantic Annotation of Field Books and Specimen Labels

Geographical and taxonomical referencing of specimens and documented species observations from within and across natural history collections is vital for ongoing species research. However, much of the historical data such as field books, diaries and specimens, are challenging to work with. They are computationally inaccessable, refer to historical place names and taxonomies, and are written in a variety of languages. In order to address these challenges and elucidate historical species observation data, we developed a workflow to (i) crowd-source semantic annotations from handwritten species observations, (ii) transform them into RDF (Resource Description Framework) and (iii) store and link them in a knowledge base. Instead of full-transcription we directly annotate digital field books scans with key concepts that are based on Darwin Core standards. Our workflow stresses the importance of verbatim annotation. The interpretation of the historical content, such a resolving a historical taxon to a current one, can be done by individual researchers after the content is published as linked open data. Through the storage of annotion provenance, who created the annotation and when, we allow multiple interpretations of the content to exist in parallel, stimulating scientific discourse. The semantic annotation process is supported by a web application, the Semantic Field Book (SFB)-Annotator, driven by an application ontology. The ontology formally describes the content and meta-data required to semantically annotate species observations. It is based on the Darwin Core standard (DwC), Uberon and the Geonames ontology. The provenance of annotations is stored using the Web Annotation Data Model. Adhering to the principles of FAIR (Findable, Accessible, Interoperable & Reusable) and Linked Open Data, the content of the specimen collections can be interpreted homogeneously and aggregated across datasets. This work is part of the Making Sense project: makingsenseproject.org. The project aims to disclose the content of a natural history collection: a 17,000 page account of the exploration of the Indonesian Archipelago between 1820 and 1850 (Natuurkundige Commissie voor Nederlands-Indie) With a knowledge base, researchers are given easy access to the primary sources of natural history collections. For their research, they can aggregate species observations, construct rich queries to browse through the data and add their own interpretations regarding the meaning of the historical content

From Handwritten Manuscripts to Linked Data

Computer Systems, Imagery and Medi

Clear vision: a step towards unravelling student recruitment in English universities?

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Purpose The recruitment of undergraduate students within English universities is of vital importance to both the academic success and the financial stability of the organisation. Despite the primacy of the task, there has been a dearth of research looking at related performance and how to ensure that the process is optimised. The purpose of this study was to investigate the degree of variation both within a university and between different universities. The reliance that individual programmes and/or universities place on the Clearing process is key; given its uncertainty, resource demands and timing shortly before students take up their places. Design/methodology/approach The Nomogramma di Gandy diagrammatical approach utilises readily available data to analyse universities’ performance in recruiting students to different programmes, and the degree to which they each rely of the Clearing process. Inter-university performance was investigated on a whole-student intake basis for a sample of English universities, representative of type and region. Findings The study found that there were disparate patterns for the many programmes within the pilot university and also disparate patterns between different types of universities across England. Accordingly, universities should internally benchmark their programmes to inform both strategic and tactical decision-making. Similarly, Universities and Colleges Admissions Service benchmarking inter-university patterns could inform the overall sector. Originality/value The approach and findings provide lessons for analysing student recruitment which could be critical to universities’ academic and financial health, in an increasingly competitive environment

OneStop:JWS Online's access point to SBML,SBGN and MIRIAM compliant annotation

We have developed an online model constructor and validator called OneStop, which is compliant with SBGN, SBML and MIRIAM standards. Key features of OneStop are: 1) a human readable input form (in addition to SBML upload and saving); 2) live visualization (SBGN graphics) of the reaction network during the construction phase; and 3) online access from any machine with a compatible browser. Sophisticated error feedback simplifies the debugging process during model construction significantly and guides the efforts of new users in a step by step fashion. OneStop is seamlessly integrated with the JWS Online model repository and simulator and also facilitates the importation of models from the BioModels database. In addition, OneStop is part of the SysMO-SEEK platform, which is used for data and model management in the Pan-European SysMO consortium