A suitcase concretely: Exploration of the Balkan immigrants’ in-between belonging through the lens of comics

Migration from peripheral European territories such as the Balkans is rarely represented and discussed in popular visual culture, despite its proliferation and impact on the economy and labour markets; there is also an overall lack of representation of Eastern European immigration in comics. The following thesis tackles one aspect of migration from the Balkans by exploring the notions of belonging within the immigrant communities. It addresses the question: what are ways in comics for depicting notions of belonging within Balkan immigrant communities? Together with the theoretical component, the thesis also contains a practical part: the comics collection of short stories "A Suitcase Concretely". The theoretical framework of the thesis engages with three vectors of research – comics studies, migration studies, and Balkan studies – connected conceptually by the theme of belonging. It contextualises the project within the sub-genre of migration comics, and overviews main tendencies of comics development in the Balkans. The framework continues by providing a historical background to key Western attitudes towards the Balkans region. Finally, it highlights main theoretical discourses related to belonging, including Etienne Wenger’s modes of belonging which have been employed as an analytical reference for the analysis. In terms of research methodology, the thesis includes case studies of "Fatherland" by Nina Bunjevac (2014), "Belonging: A German Reckons with History and Home" by Nora Krug (2018), and "Me & My Daddy & Zlatan" by Mattias Elftorp (2014). These comic works are discussed against Wenger’s modes of belonging, proving the applicability of his framework as a means of analysing affiliation sentiments within sequential art. After validating Wenger’s framework in the context of comics, the text analyses the practical component of the thesis "A Suitcase Concretely" against that same framework, thus involving further aspects of Balkan migration experiences. In conclusion, the thesis summarises examples of expressions of belonging conveyed through comics artform. It highlights angles that refer particularly to the notions relating to Balkan migrant communities. The expressions of belonging featured in the thesis are language, cultural participation, performance of labour, the everyday referral to objects which symbolise affiliations, notions and stereotypes, and interactions with institutions

Incorporating Ameriflux Data into LVT

This paper describes a new generic data reader that was developed in Fortran to handle the Ameriflux data for the LIS Verification Toolkit (LVT). Researchers at the Hydrological Sciences Branch of NASA Goddard Space Flight Center have created a high resolution land surface modeling and data assimilation system known as the Land Information System (LIS), which provides an infrastructure to integrate state-of-the-art land surface models, data assimilation algorithms, observations of land surface from satellite and remotely sensed platforms to provide estimates of land surface conditions such as soil moisture, evaporation, snowpack and runoff. These model predictions are typically evaluated by comparing them with data from observational networks. The observational data; however, are usually available in disparate data formats and require significant effort to process them into a structure amenable for use with the model data. The motivation to develop a uniform approach for land surface verification as a way to alleviate these processing efforts has led to the development of LVT which is designed to enable the rapid evaluation of land surface modeling and analysis products from LIS. LVT focuses on the use of observational datasets in their native format. As the formats of these datasets vary widely, a major part of LVT is creating programs to read and process the native datasets. The primary goal of this project is to enhance LVT capabilities by incorporating observational datasets from Ameriflu

From text to structured data: Converting a word-processed floristic checklist into Darwin Core Archive format

The paper describes a pilot project to convert a conventional floristic checklist, written in a standard word processing program, into structured data in the Darwin Core Archive format. After peer-review and editorial acceptance, the final revised version of the checklist was converted into Darwin Core Archive by means of regular expressions and published thereafter in both human-readable form as traditional botanical publication and Darwin Core Archive data files. The data were published and indexed through the Global Biodiversity Information Facility (GBIF) Integrated Publishing Toolkit (IPT) and significant portions of the text of the paper were used to describe the metadata on IPT. After publication, the data will become available through the GBIF infrastructure and can be re-used on their own or collated with other data.This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.NHM Repositor

Integrating and visualising primary data from prospective and legacy taxonomic literature.

Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovery and description, and 2) the prevalence of rarity in species descriptions

Progress in authority management of people names for collections

The concept of building a network of relationships between entities, a knowledge graph, is one of the most effective methods to understand the relations between data. By organizing data, we facilitate the discovery of complex patterns not otherwise evident in the raw data. Each datum at the nodes of a knowledge graph needs a persistent identifier (PID) to reference it unambiguously. In the biodiversity knowledge graph, people are key elements (Page 2016). They collect and identify specimens, they publish, observe, work with each other and they name organisms. Yet biodiversity informatics has been slow to adopt PIDs for people and people are currently represented in collection management systems as text strings in various formats. These text strings often do not separate individuals within a collecting team and little biographical information is collected to disambiguate collectors. In March 2019 we organised an international workshop to find solutions to the problem of PIDs for people in collections with the aim of identifying people unambiguously across the world's natural history collections in all of their various roles. Stakeholders were represented from 11 countries, representing libraries, collections, publishers, developers and name registers. We want to identify people for many reasons. Cross-validation of information about a specimen with biographical information on the specimen can be used to clean data. Mapping specimens from individual collectors across multiple herbaria can geolocate specimens accurately. By linking literature to specimens through their authors and collectors we can create collaboration networks leading to a much better understanding of the scientific contribution of collectors and their institutions. For taxonomists, it will be easier to identify nomenclatural type and syntype material, essential for reliable typification. Overall, it will mean that geographically dispersed specimens can be treated much more like a single distributed infrastructure of specimens as is envisaged in the European Distributed Systems of Scientific Collections Infrastructure (DiSSCo). There are several person identifier systems in use. For example, the Virtual International Authority File (VIAF) is a widely used system for published authors. The International Standard Name Identifier (ISNI), has broader scope and incorporates VIAF. The ORCID identifier system provides self-registration of living researchers. Also, Wikidata has identifiers of people, which have the advantage of being easy to add to and correct. There are also national systems, such as the French and German authority files, and considerable sharing of identifiers, particularly on Wikidata. This creates an integrated network of identifiers that could act as a brokerage system. Attendees agreed that no one identifier system should be recommended, however, some are more appropriate for particular circumstances. Some difficulties have still to be resolved to use those identifier schemes for biodiversity : 1) duplicate entries in the same identifier system; 2) handling collector teams and preserving the order of collectors; 3) how we integrate identifiers with standards such as Darwin Core, ABCD and in the Global Biodiversity Information Facility; and 4) many living and dead collectors are only known from their specimens and so they may not pass notability standards required by many authority systems. The participants of the workshop are now working on a number of fronts to make progress on the adoption of PIDs for people in collections. This includes extending pilots that have already been trialed, working with identifier systems to make them more suitable for specimen collectors and talking to service providers to encourage them to use ORCID iDs to identify their users. It was concluded that resolving the problem of person identifiers for collections is largely not a lack of a solution, but a need to implement solutions that already exist

A Nano(publication) Approach Towards Big Data in Biodiversity

One of the major challenges in biodiversity informatics is the generation of machine-readable data that is interoperable between different biodiversity-related data infrastructures. Producers of such data have to comply with existing standards and to be resourceful enough to enable efficient data generation, management and availability. Conversely, nanopublications offer a decentralised approach (Kuhn et al. 2016) towards achieving data interoperability in a robust and standarized way. A nanopublication is a named RDF graph, which serves to communicate a single fact and its original source (provenance) through the use of identifiers and linked data (Groth et al. 2010). It is composed of three constituent graphs (assertion, provenance, and publication info), which are linked to one another in the nanopublication header (Kuhn et al. 2016). For instance, a nanopublication has been published to assert a species interaction in which a hairy woodpecker (Picoides villosus) ate a beetle (genus Ips), along with the license and related bibliographic citation*1. In biodiversity, nanopublications can be used to exchange information between infrastructures in a standardised way (Fig. 1) and to enable curation and correction of knowledge. They can be implemented within different workflows to formalise biodiversity knowledge in self-enclosed graphs. We have developed several nanopublication models*2 for different biodiversity use cases: species occurrences, new species descriptions, biotic interactions, and links between taxonomy, sequences and institutions. Nanopublications can be generated by various means:semi-automatic extraction from the published literature with a consequent human curation and publication;generation during the publication process by the authors via dedicated formalisation tool and published together with the article;de novo generation of a nanopublication through decentralised networks such as Nanobench (Kuhn et al. 2021).One of the possible uses of nanopublications in biodiversity is communicating new information in a standardised way so that it can be accessed and interpreted by multiple infrastructures that have a common agreement on how information is expressed through the use of particular ontologies, vocabularies and sets of identifiers. In addition, we envision nanopublications to be useful for curation or peer-review of published knowledge by enabling any researcher to publish a nanopublication containing a comment of an assertion made in a previously published nanopublication. With this talk, we aim to showcase several nanopublication formats for biodiversity and to discuss the possible applications of nanopublications in the biodiversity domain

Online direct import of specimen records into manuscripts and automatic creation of data papers from biological databases

This is a Research Presentation paper, one of the novel article formats developed for the Research Ideas and Outcomes (RIO) journal and aimed at representing brief research outcomes. In this paper we publish and discuss our webinar presentation for the Integrated Digitized Biocollections (iDigBio) audience on two novel publishing workflows for biodiversity data: (1) automatic import of specimen records into manuscripts, and (2) automatic generation of data paper manuscripts from Ecological Metadata Language (EML) metadata. Information on occurrences of species and information on the specimens that are evidence for these occurrences (specimen records) is stored in different biodiversity databases. These databases expose the information via public REST API's. We focused on the Global Biodiversity Information Facility (GBIF), Barcode of Life Data Systems (BOLD), iDigBio, and PlutoF, and utilized their API's to import occurrence or specimen records directly into a manuscript edited in the ARPHA Writing Tool (AWT). Furthermore, major ecological and biological databases around the world provide information about their datasets in the form of EML. A workflow was developed for creating data paper manuscripts in AWT from EML files. Such files could be downloaded, for example, from GBIF, DataONE, or the Long-Term Ecological Research Network (LTER Network)

The Pensoft Annotator: A new tool for text annotation with ontology terms

IntroductionDigitisation of biodiversity knowledge from collections, scholarly literature and various research documents is an ongoing mission of the Biodiversity Information Standards (TDWG) community. Organisations such as the Biodiversity Heritage Library make historical biodiversity literature openly available and develop tools to allow biodiversity data reuse and interoperability. For instance, Plazi transforms free text into machine-readable formats and extracts collection data and feeds it into the Global Biodiversity Information Facility (GBIF) and other aggregators. All of these digitisation workflows require a lot of effort to develop and implement in practice. In essence, what these digitisation activities entail are the mapping of free text to concepts from recognised vocabularies or ontologies in order to make the content understandable to computers. AimWe aim to address the problem of mapping free text to ontological terms ("strings to things") with our tool for text-to-ontology mapping: the Pensoft Annotator.Methods & ImplementationThe Annotator is a web application that performs direct text matching to terms from any ontology or vocabulary list given as input to the Annotator. The term 'ontology' is used loosely here and means a collection of terms and their synonyms, where terms are uniquely identified via a Uniform Resource Identifier (URI). The Annotator accepts any of the following ontology formats (e.g. OBO, OWL, RDF/XML, etc.) but does not require the existence of a proper ontology structure (logical statements). We use the ROBOT command line tool to convert any of these formats to JSON. After the upload of a new ontology, the Annotator processes the ontology terms by normalising all exact synonyms and by removing all of the other synonyms (related, narrow and broad synonyms). This is done to limit the number of false positive matches and to preserve the semantic similarity between the matched ontology term and the text.After matching the words in the input text and the ontology term labels, the Pensoft Annotator returns a table of matched ontology terms including the following fields: the identifier of the ontology term, the ontology term label or the label of the synonym, the starting position of the matched term in the text, the term context (words surrounding the matched term in the text), the type of ontology term (class or property), the ontology from which the matched term originates and the number of times a given term is mentioned in the text. The Pensoft Annotator allows simultaneous annotation with multiple ontologies. To better visualise the exact ontology from which a matching term has been found, the terms are highlighted in different colour depending on the ontology. The Pensoft Annotator is also accessible programmatically via an Application Programming Interface (API), documented at https://annotator.pensoft.net/api.Discussion & Use CasesThe Pensoft Annotator provides functionalities that will aid the transformation of free text to collections of semantic resources. However, it still requires expert knowledge to use as the ontologies need to be selected carefully. Some false positive matches from the annotation are possible because we do not perform semantic analysis of the texts. False negatives are also possible since there might be different word forms of ontology terms, which are not direct matches to them (e.g. 'wolf' and 'wolves'). For this reason, matched terms can be reviewed and removed from the results within the web interface of the Pensoft Annotator. After removal of terms, they will not be present in the downloaded results. The Pensoft Annotator can be used to annotate biodiversity and taxonomic literature to help with the extraction of biodiversity knowledge (e.g. species habitat preferences, species interaction data, localities, biogeographic data). The existence of some domain and taxon-specific ontologies, such as the Hymenoptera Anatomy Ontology, provides further opportunities for context-specific annotation. Semantic analysis of unstructured texts could be applied in addition to ontology annotation to improve the accuracy of ontology term matching and to filter out mismatched terms. Annotation of structured or semi-structured text (e.g. tables) can be done with better success. A recent example demonstrates the use of the Annotator to extract biotic interactions from tables (Dimitrova et al. 2020). The Annotator could also be used for ontology analysis and comparison. Annotation of text can help to discover gaps in ontologies as well as inaccurate synonyms. For instance, a certain word could be recognised as an ontology term match because it is an exact synonym in the ontology but in reality it might be more accurate to mark it as a related synonym. In addition, annotation with multiple ontologies can help to elucidate links between ontologies

Accelerating innovative publishing in taxonomy and systematics: 250 issues of ZooKeys

Since its launch on the 4th of July 2008 until 2012 the ZooKeys journal has been showing a constant growth and advancement in editorial workflow, constantly implementing new and improved publishing and dissemination technologies. This Editorial explores how 2012 was an important year in the development of Zookeys and how this year contributed to the 4 years of positive experience