bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uniquely Identifying Collectors of Specimens
Authors: Groom Quentin , Dillen Mathias , Huybrechts Pieter 
Published: June 2019

Being able to connect together the specimens collected and determined by a person is key to understanding the origins, history, identity and ownership of a collection. Yet making these connections is difficult because people’s names change, are not unique and are written in many different ways. Semantic annotation of people names with stable identifiers is a solution to this problem.
Semantic annotation requires the linking of textual information to unique identities for known entities. This often needs to be done manually and can be time-consuming and error-prone. We have been linking person text strings to persistent identifiers of various kinds. We focused on the semantic annotation of people names mentioned on specimen labels, particularly the collectors, but also determiners of the specimen. Various person identifiers systems exist and they vary in their scope, their business model and their notability requirements. We have chosen, where possible, to link to several systems, because we feel this creates a more robust system, that does not rely on the maintenance of any single identifier system.
Currently, we are using Virtual International Authority File (VIAF) identifiers that are particularly useful for published authors. The Harvard University Index of Botanists has information on well known botanists and ORCID IDs are useful for living collectors. However, even with all these various identifiers systems, there are many collectors of whom we know little, particularly where they have not published or done something notable other than collect specimens. For many of these collectors Wikidata is a solution, because it can be edited by anyone and because it has a low threshold for notability. Wikidata also has the additional advantage of forming a bridge between many identifier systems. Hence, we incorporated Wikidata entries as well if available and endeavoured to merge existing duplicates wherever we could. In this process, we have examined the coverage, scope and reliability of these different systems for identifying collectors and determiners. We also advise on strategies for linking collectors to their identifiers efficiently. Linking specimens to clearly identified people has enormous advantages for specimen data curation and linking between different collections. We encourage every collection to prioritize this.
Progress in Construction of Animal Trait Ontologies
Authors: Wang Jiangning , Lin Congtian , Han Yan , Huang Xiongwei , Xi TianYu , Wang Zhaojun , Ji Liqiang 
Published: June 2019

Extracting and formulating an animal trait ontology is the basis of building a trait database. The character selection from existing traditional biodiversity databases is limited and biased by the information already in a collection. With the increasing amount of character data and the advance of character information acquisition projects, the success of making animal trait ontologies or specifications of terms is imminent.
According to the general workflow of our ontology project, after investigating a large number of biodiversity databases, we extracted relatively complete character terms from dictionaries, training handbooks, journals and classical textbooks, and then constructed relationships according to some rules to form a preliminary animal trait ontology. When formulating the domain ontology/specification, our process is as follows:

Select the group and related materials; select the "specification" as the starting point of work; and then supplement with the teaching materials, journal citations and dictionaries of the relevant group for reference;

Extract terms from multiple sources, so only a few additions and modifications are needed after the second time;

Make structural adjustments to all terms according to the specification of description sequence;

Invite experts to examine and approve the project and repeat steps 2 and 3 (sometimes beginning from step 1) according to their opinions until they are approved.

Select the group and related materials; select the "specification" as the starting point of work; and then supplement with the teaching materials, journal citations and dictionaries of the relevant group for reference;
Extract terms from multiple sources, so only a few additions and modifications are needed after the second time;
Make structural adjustments to all terms according to the specification of description sequence;
Invite experts to examine and approve the project and repeat steps 2 and 3 (sometimes beginning from step 1) according to their opinions until they are approved.
At present, we have completed the construction of terms and their relationships for a morphological description of feature ontologies in birds, mammals, insects (only Lepidoptera), amphibians and reptiles. While constructing such morphology / taxonomy-based ontologies, we also formulated their attributes, which are supplemented by ontologies in various fields. All these terms are undergoing the second review by domain experts.
Although the existing work is only one small tip of the iceberg of the whole zoological trait ontology project, it is of great public interest. Compared with existing ontologies such as OBA (ontology of biological attributes, for development researchers) and UBERON (for surgeons), our ontologies are more suitable for taxonomists and biodiversity researchers.
The Biodiversity Informatics Training Curriculum (BITC): Versions 1 and 2
Authors: Ingenloff Kate , Saupe Erin , Townsend Peterson Andrew 
Published: June 2019

Beginning in 2012, the JRS Biodiversity Foundation funded the University of Kansas to carry out a series of courses covering the breadth of the field of biodiversity informatics in cities across Africa. The Biodiversity Informatics Training Curriculum (BITC) was created from these events that used in-person courses taught by world experts in biodiversity informatics fields. The courses reached 120+ students and young professionals from 23 countries across Africa, and the digital videos of the courses reached thousands of viewers and users worldwide. BITC1 concluded in 2015 and a biodiversity informatics "curriculum" was published in the form of a compendium of BITC course materials (Peterson and Ingenloff 2016)—this curriculum has now been used as the basis for multiple programs of study around the world. BITC2 is now funded, again thanks to the JRS Biodiversity Foundation—this second version involves longer, more thematically oriented courses to be held in three east and southern African countries. The first will be held in Rwanda, in September 2019, and will focus on "Measuring Essential Biodiversity Variables and Ecosystem Services." BITC2 courses will begin with an open symposium, and then will proceed with intensive, hands-on, goal-oriented workshops with a small number of participants.
The overall objective of the BITC is a community-oriented and community-run set of training events that can provide avenues to advanced study, international collaboration, and region-wide integration of efforts in biodiversity informatics. BITC2 has four main goals:

implement new training dimensions in both an open symposium forum and an intensive, goal-and-product-focused approach that we tested in the later courses of BITC1;

expand access to learning resources via subtitling and translation;

build collaborative BITC communities via social media platforms; and

build within-Africa capacity in biodiversity informatics via high-level involvement of a number of African scientists and educators.

implement new training dimensions in both an open symposium forum and an intensive, goal-and-product-focused approach that we tested in the later courses of BITC1;
expand access to learning resources via subtitling and translation;
build collaborative BITC communities via social media platforms; and
build within-Africa capacity in biodiversity informatics via high-level involvement of a number of African scientists and educators.
These goals will be achieved via three, once-yearly symposium/course combination events which will be organized and implemented by combined leadership teams from the UK, USA, and African countries, and are intended to provide a combined total of 30-33 days of training to 36-42 trainees. Here we present the format of the BITC1 and BITC2 courses, and the positive and negative outcomes that have resulted, with an eye to optimal design of future such initiatives.
The Plazi Workflow: The PDF prison break for biodiversity data
Authors: Agosti Donat , Catapano Terry , Sautter Guido , Egloff Willi 
Published: June 2019

The Swiss NGO Plazi (http://plazi.org) has developed an automated workflow for liberating data, including images and text, from new taxonomic publications issued in PDF format. This stepwise process extracts, article metadata, illustrations and their captions, bibliographic references, scientific names, named geographic entities such as coordinates and country names, collection codes, and finally, taxonomic treatments. These extracted data are enhanced and published in TreatmentBank (http://plazi.org) and deposited in Biodiversity Literature Repository (https:/biolitrepo.org) respectively, in which a Digital Object Identifier (DataCite DOI) is minted for articles as well as their contained figures and taxon treatments, each linked to each other in their metadata. This input is complemented by the import of Journal Article Tag Suite/Taxpub XML based publications from Pensoft publishers (e.g. Zookeys, Journal of Hymenoptera Research; https://pensoft.net/browse_journals) that are semantically enhanced during their journal production workflow. Upon import, materials citation are discovered and parsed, and the taxonomic treatments added to TreatmentBank where a persistent identifier is minted. From TreatmentBank data from taxonomic treatments, including occurence data from cited specimens, are submitted to GBIF (http://gbif.org), or are accessible via API. Treatments and material citations from more than 26,200 articles have been registered. The articles can be found on GBIF using the Digital Object Identifier in the search field.
Plazi, together with Pensoft Publishers, has processed over 26,000 articles containing more than 284,000 taxonomic treatments, 190,000 images, 50,000 georeferenced materials citations, together comprising an estimated 100 million facts. Through the support of the Arcadia Fund (https://www.arcadiafund.org.uk/) Plazi's processing is expanding to cover a sufficient number of journals to liberate the data of over 50% of the new described animal species annually. This will complement an existing service provided to the Muséum National d’Histoire Naturelle, Paris, to convert the European Journal of Taxonomy and their other journals (http://sciencepress.mnhn.fr/en/periodiques/adansonia/40/1) to JATS/TaxPub (https://www.ncbi.nlm.nih.gov/books/NBK47081), as well as an increasing portfolio of journals published in JATS/TaxPub by Pensoft Ltd.
From Expert to Data-Driven Biodiversity Knowledge: Assessing ecosystem irreplaceability with IUCN Red List data for freshwater fish
Authors: Miqueleiz Imanol , Ariño Arturo H. , Miranda Rafael 
Published: June 2019

Critical as they are for humans and nature, freshwater ecosystems are threatened—but the extent and depth of these threats are not well understood, especially if essential biodiversity data are lacking. Any policy aimed at protecting such ecosystems must first assess the threat factors and the potential harm, well before proposing conservation measures such as the creation and development of Protected Areas (PAs). These assessments must be done using a deep and sound knowledge of the actual and potential biodiversity variables. Freshwater ecosystems have been largely neglected in traditional PA design and management (Abell et al. 2007), be it for scarcity of biodiversity data, or for more perception-related reasons such as visibility and accessibility driving the allocation of conservation resources to more data-rich environments.
In an effort to contribute to shifting this state of affairs, we have developed an irreplaceability index to identify the most relevant places to achieve conservation aims for freshwater fish, based on the International Union for the Conservation of Nature (IUCN) Red List, which, in turn, should be founded on available biodiversity data upon which expert knowledge is based (Le Saout 2013). However, we found large assessment gaps in the IUCN Red List for freshwater fish. These gaps may result from the non-systematic acquisition of primary biodiversity data, which could eventually be alleviated by coordinated policies promoting ecosystem surveys tailored at increasing the availability and spread of such data, while identifying, targeting and prioritizing hotspots. Obtaining valid conclusions from low-assessment areas such as South America, which are simultaneously biodiversity and endangerment hotspots (Collen 2014), is particularly troublesome.
Building an irreplaceability index requires access to abundant, fine-scale biodiversity data. When combined with the assessment information available in the IUCN Red List, we can identify those areas where low assessment rates for highly irreplaceable rivers become keystones to protect freshwater biodiversity, and can therefore suggest actions for policy makers to take at both regional and local scales. In particular, we have thus identified those irreplaceable rivers that fall outside the current net of PAs. In a context of inadequate investment in biodiversity conservation (Juffe-Bignoli et al. 2016), our findings and the informatics-powered methods we propose, will hopefully help decision makers establish conservation priorities and allocate funds to preserve irreplaceable rivers and their fish fauna. Furthermore, the necessity of improving the IUCN Red List in low-assessed areas, requires synergies among IUCN, Global Biodiversity Information Facility (GBIF) and conservation scientists to achieve accurate and reliable assessments.
Towards an Ontology of Comparative Biogeography: New insights into the semantics of biodiversity conservation
Authors: Ung Visotheary , Buttigieg Pier Luigi 
Published: June 2019

Climate change, habitat destruction, and myriad other ecological stressors will impact us all and have already contributed to what is being labeled the sixth wave of extinction (Ceballos et al. 2015, Régnier et al. 2015). As a countering force, conservation biology strives to identify those areas of the planet most worthy of protecting due to their unique natural value (Dudley and Stolton 2008). Despite their value, criticisms (Camillo and Peter 2011) have been leveled at 1) the social cost of maintaining protected status (Lele et al. 2010) and 2) instances of continued biodiversity decline despite protection regimes (Craigie et al. 2010, Dudley et al. 2014). At present, the selection and delimitation of protected areas is an intuitive and often subjective process, leading to ambiguities in the semantics behind and across their definitions.
Thus, we propose that the application of ontological techniques to the ambiguities in protected area semantics is a timely contribution to conservation informatics. We hold that coherent semantic representation of the biogeographic areas which overlap protected areas (often designated empirically) will provide more efficient and standardized informatics, supporting research and decision-making processes. Our approach draws from comparative biogeography, which seeks to classify biogeographic areas based on their natural properties in a process known as bioregionalisation. In particular, we convert a cladogram of biogeographic areas (similar to cladogram of taxa) into a series of ontological classes, each corresponding to a monophyletic clade of areas. In this model, areas of endemism are treated as formal objects related by hierarchical relationships and constrained by the monophyly condition (Ung 2018). This approach unifies a model-theoretic view of endemism with the semantic web and therefore, offering new possibilities to communicate the biogeographic units conservation.
We use semantic web standards (RDF and OWL) expressed through interoperable "Open Biological and Biomedical Ontology (OBO) Foundry" and Library resources to model areas of endemism as evolutionary entities for comparative biogeography. This aligns with current efforts in the OBO Foundry to extend their semantic coverage to the domains of Earth and ecosystem science. Due to our work’s heavy reliance on environmental semantics, we base our work on the Environment Ontology (ENVO), extending it with often confounded biogeographic entities including biogeographic areas, such as areas of endemism and endemic areas, as well as their relationships. Hence, we seek to provide a rigorous and simple framework that improves biogeographic analyses and interoperability between systems.
Sepsis-Induced State of Immunoparalysis Is Defined by Diminished CD8 T Cell–Mediated Antitumor Immunity
Authors: Danahy Derek B. , Kurup Samarchith P. , Winborn Christina S. , Jensen Isaac J. , Harty John T. , Griffith Thomas S. , Badovinac Vladimir P. 
Published: June 2019

Abstract
Patients who survive sepsis experience long-term immunoparalysis characterized by numerical and/or functional lesions in innate and adaptive immunity that increase the host’s susceptibility to secondary complications. The extent to which tumor development/growth is affected in sepsis survivors remains unknown. In this study, we show cecal ligation and puncture (CLP) surgery renders mice permissive to increased B16 melanoma growth weeks/months after sepsis induction. CD8 T cells provide partial protection in this model, and tumors from sepsis survivors had a reduced frequency of CD8 tumor-infiltrating lymphocytes (TILs) concomitant with an increased tumor burden. Interestingly, the postseptic environment reduced the number of CD8 TILs with high expression of activating/inhibitory receptors PD-1 and LAG-3 (denoted PD-1hi) that define a tumor-specific CD8 T cell subset that retain some functional capacity. Direct ex vivo analysis of CD8 TILs from CLP hosts showed decreased proliferation, IFN-γ production, and survival compared with sham counterparts. To increase the frequency and/or functional capacity of PD-1hi CD8 TILs in tumor-bearing sepsis survivors, checkpoint blockade therapy using anti–PD-L1/anti–LAG-3 mAb was administered before or after the development of sepsis-induced lesions in CD8 TILs. Checkpoint blockade did not reduce tumor growth in CLP hosts when therapy was administered after PD-1hi CD8 TILs had become reduced in frequency and/or function. However, early therapeutic intervention before lesions were observed significantly reduced tumor growth to levels seen in nonseptic hosts receiving therapy. Thus, sepsis-induced immunoparalysis is defined by diminished CD8 T cell–mediated antitumor immunity that can respond to timely checkpoint blockade, further emphasizing the importance of early cancer detection in hosts that survive sepsis.
Choosing Wisely, the reasons for its success
Authors: Bobbio Marco , Vernero Sandra 
Published: June 2019

The philosophy and the history of the International Choosing Wisely movement, launched in the U.S. in 2012, are described. It grew and spread beyond what it was anticipated at the beginning because there is a rising concern of the medical community regarding the appropriate use of procedures and treatments placed into the market before an adequate evaluation of risks and benefits. Not only healthcare providers, but also patients, citizens and politicians, are becoming aware of the consequences of inappropriate decisions and behaviors since inappropriateness has economic (waste of resources), clinical (risks), but also ethical implications. In Italy the movement was launched and still is coordinated by the Slow Medicine organization, that created the campaign Doing more does not mean doing better – Choosing Wisely Italy, which aimed to improve clinical appropriateness through the reduction of unnecessary tests and treatments and the dialogue between physicians and patients. Currently, 44 societies of physicians, nurses, pharmacists and physiotherapists identified 230 recommendations about tests, treatments and procedures commonly used in Italy’s clinical practice that do not provide any benefit to most patients but may cause harm.
What is so theological about a faculty of theology at a public university? Athens – Berlin – Pretoria
Authors: Buitendag Johan 
Published: June 2019

In this article, the author engages with the question ‘what is so theological about theological education?’, which he calls a genealogy of theology. This matter is approached from a very specific vantage point as the author was the former dean of the Faculty of Theology and Religion at the University of Pretoria (South Africa) and has engaged in this research project over the past 5 years, as the Faculty was under severe review as to its composition, and ultimately its very future. This article endeavours to bring to the surface the underlying theology of the author and the paradigm he is operating from. It concludes with a definition of theology as he sees it, but with the explicit qualification of it being situated at a research-intensive university competing for a notable position on the ranking indexes of world universities. A new niche is thus opening up for theology (vis-à-vis a seminary or even a Christian university), namely, a ‘scholarly endeavour of believers in the public sphere in order to inquire into a multi-dimensional reality in a manner that matters’.
Auto-memorialisation: Augustus’ Res Gestae as slanted narrative
Authors: Claassen Johanna Maria 
Published: June 2019

That Augustus wanted to utilise the to-be-publicly-published record of his career, the Res Gestae Divi Augusti, as subtle propaganda, is a well-established critical assumption. While never blatantly inventing ‘facts’ about his many achievements, the emperor manipulated his brief narrations of individual achievements to fit in with his programme of propaganda. This article not so much explores the ‘facts’ behind Augustus’ categorical assertions of achievements in many spheres, but analyses stylistically his presentation of these facts and his narrative strategies. The exiled poet, Ovid, is shown as one of the first critical readers of the document, his apparent allusions to it seemingly exposing Augustus’ often tendentious manipulation of the contrast between ‘what happened’ and ‘how it is told’. The article ends with reference to another critical reader of Augustus’ slanted auto-memorialisation.