Is searching full text more effective than searching abstracts?

Background  

With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the following question: is searching full text more effective than searching abstracts? This question is answered by comparing text retrieval algorithms on MEDLINE^? abstracts, full-text articles, and spans (paragraphs) within full-text articles using data from the TREC 2007 genomics track evaluation. Two retrieval models are examined: bm25 and the ranking algorithm implemented in the open-source Lucene search engine.     

The WISER metadatabase: the key to more than 100 ecological datasets from European rivers, lakes and coastal waters

In ecological sciences, the role of metadata (i.e. key information about a dataset) to make existing datasets visible and discoverable has become increasingly important. Within the EU-funded WISER project (Water bodies in Europe: Integrative Systems to assess Ecological status and Recovery), we designed a metadatabase to allow scientists to find the optimal data for their analyses. An online questionnaire helped to collect metadata from the data providers and an online query tool (http://www.wiser.eu/results/meta-database/) facilitated data evaluation. The WISER metadatabase currently holds information on 114 datasets (22 river, 71 lake, 1 general freshwater and 20 coastal/transitional datasets), which also can be accessed by external scientists. We evaluate if generally used metadata standards (e.g. Darwin Core, ISO 19115, CSDGM, EML) are suitable for such specific purposes as WISER and suggest at least the linkage with standard metadata fields. Furthermore, we discuss whether the simple metadata documentation is enough for others to reuse a dataset and why there is still reluctance to publish both metadata and primary research data (i.e. time and financial constraints, misuse of data, abandoning intellectual property rights). We emphasise that metadata publication has major advantages as it makes datasets detectable by other scientists and generally makes a scientist’s work more visible.     

Proposed Standards for Variable Harmonization Documentation and Referencing: A Case Study Using QuickCharmStats 1.1

Comparative statistical analyses often require data harmonization, yet the social sciences do not have clear operationalization frameworks that guide and homogenize variable coding decisions across disciplines. When faced with a need to harmonize variables researchers often look for guidance from various international studies that employ output harmonization, such as the Comparative Survey of Election Studies, which offer recoding structures for the same variable (e.g. marital status). More problematically there are no agreed documentation standards or journal requirements for reporting variable harmonization to facilitate a transparent replication process. We propose a conceptual and data-driven digital solution that creates harmonization documentation standards for publication and scholarly citation: QuickCharmStats 1.1. It is free and open-source software that allows for the organizing, documenting and publishing of data harmonization projects. QuickCharmStats starts at the conceptual level and its workflow ends with a variable recording syntax. It is therefore flexible enough to reflect a variety of theoretical justifications for variable harmonization. Using the socio-demographic variable ‘marital status’, we demonstrate how the CharmStats workflow collates metadata while being guided by the scientific standards of transparency and replication. It encourages researchers to publish their harmonization work by providing researchers who complete the peer review process a permanent identifier. Those who contribute original data harmonization work to their discipline can now be credited through citations. Finally, we propose peer-review standards for harmonization documentation, describe a route to online publishing, and provide a referencing format to cite harmonization projects. Although CharmStats products are designed for social scientists our adherence to the scientific method ensures our products can be used by researchers across the sciences.     

History in the Gene: Negotiations Between Molecular and Organismal Anthropology

In the advertising discourse of human genetic database projects, of genetic ancestry tracing companies, and in popular books on anthropological genetics, what I refer to as the anthropological gene and genome appear as documents of human history, by far surpassing the written record and oral history in scope and accuracy as archives of our past. How did macromolecules become “documents of human evolutionary history”? Historically, molecular anthropology, a term introduced by Emile Zuckerkandl in 1962 to characterize the study of primate phylogeny and human evolution on the molecular level, asserted its claim to the privilege of interpretation regarding hominoid, hominid, and human phylogeny and evolution vis-à-vis other historical sciences such as evolutionary biology, physical anthropology, and paleoanthropology. This process will be discussed on the basis of three key conferences on primate classification and evolution that brought together exponents of the respective fields and that were held in approximately ten-years intervals between the early 1960s and the 1980s. I show how the anthropological gene and genome gained their status as the most fundamental, clean, and direct records of historical information, and how the prioritizing of these epistemic objects was part of a complex involving the objectivity of numbers, logic, and mathematics, the objectivity of machines and instruments, and the objectivity seen to reside in the epistemic objects themselves.     

From theory to data: Representing neurons in the 1940s

Recent literature on the role of pictorial representation in the life sciences has focused on the relationship between detailed representations of empirical data and more abstract, formal representations of theory. The standard argument is that in both a historical and epistemic sense, this relationship is a directional one: beginning with raw, unmediated images and moving towards diagrams that are more interpreted and more theoretically rich. Using the neural network diagrams of Warren McCulloch and Walter Pitts as a case study, I argue that while in the empirical sciences, pictorial representation tends to move from data to theory, in areas of the life sciences that are predominantly theoretical, when abstraction occurs at the outset, the relationship between detail and abstraction in pictorial representations can be of a different character.     

Species of natural hybrid origin and misinformation in the Irises: A reappraisal of the presence of I. aphylla L. in Italy

Abstract

The identity and status of the records of Iris aphylla L. for Italy are reconsidered. The authors are of the opinion that I. perrieri Simonet ex N. Service, present in Savoy, France, is genetically and morphologically distinct from I. aphylla, and that the Italian populations from Piemonte are in fact conspecific with I. perrieri. In addition, we consider that another iris, I. benacensis A. Kern. ex Stapf , which occurs near Lago di Garda (Mt. Brione) and is often also regarded as a synonym of I. aphylla, is not conspecific with either I. aphylla or I. perrieri. Macro-, micro-morphological and biosystematic data obtained during this investigation suggest a possible natural hybrid origin of these species and confirm the opinion of the authors, which is justified also by the different chromosome numbers and distribution of the taxa examined.     

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale

Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a ‘Big Data’ approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence‐only or presence–absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi‐source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter‐ or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi‐source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA‐based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.     

Metadata Made Easy: Develop and Use Domain‐Specific Metadata Schemes by following the dmdScheme approach

1. Metadata plays an essential role in the long‐term preservation, reuse, and interoperability of data. Nevertheless, creating useful metadata can be sufficiently difficult and weakly enough incentivized that many datasets may be accompanied by little or no metadata. One key challenge is, therefore, how to make metadata creation easier and more valuable. We present a solution that involves creating domain‐specific metadata schemes that are as complex as necessary and as simple as possible. These goals are achieved by co‐development between a metadata expert and the researchers (i.e., the data creators). The final product is a bespoke metadata scheme into which researchers can enter information (and validate it) via the simplest of interfaces: a web browser application and a spreadsheet.
2. We provide the R package dmdScheme (dmdScheme: An R package for working with domain specific MetaData schemes (Version v0.9.22), 2019) for creating a template domain‐specific scheme. We describe how to create a domain‐specific scheme from this template, including the iterative co‐development process, and the simple methods for using the scheme, and simple methods for quality assessment, improvement, and validation.
3. The process of developing a metadata scheme following the outlined approach was successful, resulting in a metadata scheme which is used for the data generated in our research group. The validation quickly identifies forgotten metadata, as well as inconsistent metadata, therefore improving the quality of the metadata. Multiple output formats are available, including XML.
4. Making the provision of metadata easier while also ensuring high quality must be a priority for data curation initiatives. We show how both objectives are achieved by close collaboration between metadata experts and researchers to create domain‐specific schemes. A near‐future priority is to provide methods to interface domain‐specific schemes with general metadata schemes, such as the Ecological Metadata Language, to increase interoperability.

The article describes a methodology to develop, enter, and validate domain specific metadata schemes which is suitable to be used by nonmetadata specialists. The approach uses an R package which forms the backend of the processing of the metadata, uses spreadsheets to enter the metadata, and provides a server based approach to distribute and use the developed metadata schemes.     

Climate change‐linked range expansion of Nathusius’ pipistrelle bat,Pipistrellus nathusii (Keyserling & Blasius, 1839)

Aim To examine the effect of climate change on the occurrence and distribution of Pipistrellus nathusii (Nathusius’ pipistrelle) in the United Kingdom (UK). Location We modelled habitat and climatic associations of P. nathusii in the UK and applied this model to the species’ historical range in continental Europe. Methods A binomial logistic regression model was constructed relating the occurrence of P. nathusii to climate and habitat characteristics using historical species occurrence records (1940–2006) and CORINE land cover data. This model was applied to historical and projected climate data to examine changes in suitable range (1940–2080) of this species. We tested the predictive ability of the model with known records in the UK after 2006 and applied the model to the species’ known range in Europe. Results The distribution of P. nathusii was related positively to the area of water bodies, woodland and small areas of urbanization, and negatively related to the area of peat/heathland. Species records were associated with higher minimum temperatures, low seasonal variation in temperature and intermediate rainfall. We found that suitable areas have existed in the UK since the 1940s and that these have expanded. The model had high predictive power when applied to new records after 2006, with a correct classification rate of 70%, estimated by receiver operating characteristic analysis. Based on climate projections, our model suggests a potential twofold increase in the area suitable for P. nathusii in the UK by 2050. The single most influential climate variable contributing to range increase was the projected increase in minimum temperature. When applied to Europe, the model predictions had best predictive capability of known records in western areas of the species’ range, where P. nathusii is present during the winter. Main conclusions We show that a mobile, migratory species has adapted its range in response to recent climate change on a continental scale. We believe this may be the first study to demonstrate a case of range change linked to contemporary climate change in a mammal species in Europe.     

Exposing hidden endemism in a Neotropical forest raptor using citizen science

Gaps in our knowledge of the geographical distribution of species represent a fundamental challenge to biogeographers and conservation biologists alike, and are particularly pervasive in the tropics. Here we highlight the case of the Rufous‐thighed Kite Harpagus diodon, a South American raptor commonly mapped as resident across half the continent. Recent observations at migration watch points have indicated it may be partially migratory in the southernmost parts of its range. To investigate this possibility, we collated contemporary and historical specimen records, published sight records and ‘digital vouchers’ – photographs and sound‐recordings archived online (from citizen science initiatives) – and explored the spatiotemporal distribution of records. We were unable to trace any documented records of this species from Amazonia during the austral summer (October–March), or records from the Atlantic Forest biome during the peak of the Austral winter (June–August), and all proven breeding records stem from the Atlantic Forest region. We compared this pattern with that of a ‘control’ species, the congeneric Double‐toothed Kite H. bidentatus, again using specimens and digital vouchers. For this species we found no evidence of seasonality between biomes and can disregard spatiotemporal variation in observer effort as a cause of seasonal biases. We consider that all populations of Rufous‐thighed Kites are fully migratory, wintering in Equatorial forests in the Amazonian basin. We provide evidence that this pattern was previously obscured by erroneous undocumented records and poor or erroneous specimen metadata, and its discovery was primarily facilitated by digital vouchers. This discovery requires a reassessment of the species’ global conservation status as an Atlantic Forest breeding endemic, threatened by habitat loss and degradation, as it was previously considered to be resident across large swathes of undisturbed Amazonian Forest on the Guiana Shield. The bulk of the digital voucher data used to elucidate this pattern were extracted from a Brazilian citizen science initiative WikiAves, which may serve as a model for collating biodiversity data in megadiverse countries and help catalyse environmental awareness.     

Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata,Ciliophora)

Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN‐BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN‐BC proposes to populate The Ciliate Guide, an online database, with biodiversity‐related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.     

Calculating life? Duelling discourses in interdisciplinary systems biology

A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences.     

Dietary Differences Among Sympatric Callitrichinae in Northern Bolivia: Callimico goeldii,Saguinus fuscicollis and S. labiatus

Studies of sympatric species can provide important data to define how dietary and habitat requirements differ among them. I collected dietary data during a first yearlong comparative study of wild groups of Callimico goeldii, Saguinus labiatus and S. fuscicollis. Dietary overlap was highest between Saguinus fuscicollis and Saguinus labiatus throughout the year, and lowest between Saguinus labiatus and Callimico goeldii. All three species had high dietary overlap in February and March when a few abundant fruit species dominated their diets. Although all three species rely heavily on many of the same fruits and arthropods, there are several important distinctions among their diets. Surprisingly, Callimico goeldii consume large quantities of fungus throughout the year: 29% of annual feeding records. Mycophagy is more frequent in the dry season when fruits are scarce. In contrast, Saguinus labiatus rarely eat fungus during the period of fruit scarcity, and instead rely on nectar, a resource never exploited by Callimico goeldii. Saguinus fuscicollis also rely on nectar during periods of low fruit availability and increase their intake of arthropods and exudates. During April, a period of fruit scarcity, exudates comprise >50% of the feeding records of Saguinus fuscicollis. The use of different food resources during fruit scarcity, and differences in the heights at which each species feeds and forages appear to define a distinct ecological niche for each of them and allow them to maintain long-term associations throughout the year. Furthermore, I hypothesize that the limited distribution of Callimico goeldii may result from their restriction to forests that have high disturbance rates, where microhabitats appropriate for fungal growth are abundant, but which also contain abundant fruit and insects.     

The UEMS Section/Board of Pathology,Chapter 6: Requirement for Recognition of Postgraduate Training in Pathology: a presentation of the Paris Document

M. Tötsch, C. Cuvelier, L. Vass and A. Fassina and on behalf of the participants of the UEMS Section/Board of Pathology meeting in Paris 2012
The UEMS Section/Board of Pathology, Chapter 6: Requirement for Recognition of Postgraduate Training in Pathology: a presentation of the Paris Document After more than five years discussion the UEMS Section/Board of Pathology agreed a specification of requirements for recognition of post‐graduate training in pathology, which is the key to the future of our discipline. The document published here, subject to ratification by UEMS Council, was voted on and accepted by the Pathology Board at the UEMS Paris meeting of 9 June 2012. Cytopathology is regarded as integral part of pathology: in general, training in pathology takes five years and maintains a common trunk of four (minimum three) years where surgical pathology, autopsy pathology and basic knowledge of neuropathology, dermatopathology and cytopathology are adequately trained and assessed. Training in so‐called ‘areas of interests’ covers the remaining 12–24 months. Certificates of ‘advanced level of competence’ remain within the authority of national boards. As senior members of its Executive Board, we believe that the European Federation of Cytology Societies (EFCS) should take responsibility for establishing 1) standards in the quality of cytopathology training, 2) training guidelines and qualification for advanced levels of competence in cytopathology, 3) manpower planning, 4) tutorials for pathologists and cytotechnologists and 4) standards of cytotechnologist training.