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Wikidata as a semantic framework for the Gene Wiki initiative

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Open biological data are distributed over many resources making them challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia.

In order to improve the state of biological data, facilitate data management and dissemination, we imported all human and mouse genes, and all human and mouse proteins into Wikidata.

In total, 59 721 human genes and 73 355 mouse genes have been imported from NCBI and 27 306 human proteins and 16 728 mouse proteins have been imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, our corpus of imported data serves as the starting point for integration of further data by scientists, the Wikidata community and citizen scientists alike.

The first use case for these data is to populate Wikipedia Gene Wiki infoboxes directly from Wikidata with the data integrated above. This enables immediate updates of the Gene Wiki infoboxes as soon as the data in Wikidata are modified.

Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for usage of the data we imported in all 280 different language Wikipedias.

Apart from the Gene Wiki infobox use case, a SPARQL endpoint and exporting functionality to several standard formats (e.g. JSON, XML) enable use of the data by scientists.

In summary, we created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data. This resource enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web.

URL : Wikidata as a semantic framework for the Gene Wiki initiative

DOI : 10.1093/database/baw015

Current state of open access to journal publications from the University of Zagreb School of Medicine

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AIMS

To identify the share of open access (OA) papers in the total number of journal publications authored by the members of the University of Zagreb School of Medicine (UZSM) in 2014.

METHODS

Bibliographic data on 543 UZSM papers published in 2014 were collected using PubMed advanced search strategies and manual data collection methods. The items that had “free full text” icons were considered as gold OA papers.

Their OA availability was checked using the provided link to full-text. The rest of the UZSM papers were analyzed for potential green OA through self-archiving in institutional repository. Papers published by Croatian journals were particularly analyzed.

RESULTS

Full texts of approximately 65% of all UZSM papers were freely available. Most of them were published in gold OA journals (55% of all UZSM papers or 85% of all UZSM OA papers). In the UZSM repository, there were additional 52 freely available authors’ manuscripts from subscription-based journals (10% of all UZSM papers or 15% of all UZSM OA papers).

CONCLUSION

The overall proportion of OA in our study is higher than in similar studies, but only half of gold OA papers are accessible via PubMed directly. The results of our study indicate that increased quality of metadata and linking of the bibliographic records to full texts could assure better visibility. Moreover, only a quarter of papers from subscription-based journals that allow self-archiving are deposited in the UZSM repository.

We believe that UZSM should consider mandating all faculty members to deposit their publications in UZSM OA repository to increase visibility and improve access to its scientific output.

URL : http://www.ncbi.nlm.nih.gov/pubmed/26935617

Open Access Publishing in Higher Education: Charting the Challenging Course to Academic and Financial Sustainability

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The benefits, pitfalls, and sustainability of open access publishing are hotly debated. Commercial publishers dominate the marketplace and oppose alternative publishing models that threaten their bottom line. Scholars’ use of open access remains relatively limited due to awareness and perceived benefits to their professional goals.

Readership of open access publications is generally strong, but some people disagree that more readers leads to increased citations and research impact. Libraries have grown their influence by supporting and promoting open access, but these efforts come with significant financial costs.

Today, open access has flourished most significantly as a philosophy: the belief that the world’s scholarship should be freely available to readers and that publicly funded research, in particular, should be accessible to the taxpayers who paid for it.

Transforming a moral good into a sustainable publishing model rests with lawmakers, scholars, and institutions of higher education. Without laws designed to ensure participation by authors and publishers, Green Open Access cannot effectively replace journal subscriptions.

Scholars need to call upon each other to archive their work, utilize open access repository web sites to find quality content, and embrace Gold Open Access journals as a professionally beneficial publishing venue.

Institutions must allocate additional internal resources to spur more and better institutional and disciplinary archives, new Gold Open Access journals, and myriad other professional, technical, and financial services necessary to promote open access as a fiscally and academically sustainable publishing solution.

URL : http://cedar.wwu.edu/jec/vol10/iss1/5/

Researchers’ Adoption of an Institutional Central Fund for Open-Access Article-Processing Charges : A Case Study Using Innovation Diffusion Theory

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This article analyzes researchers’ adoption of an institutional central fund (or faculty publication fund) for open-access (OA) article-processing charges (APCs) to contribute to a wider understanding of take-up of OA journal publishing (“Gold” OA). Quantitative data, recording central fund usage at the University of Nottingham from 2006 to 2014, are analyzed alongside qualitative data from institutional documentation.

The importance of the settings of U.K. national policy developments and international OA adoption trends are considered. Innovation Diffusion Theory (IDT) is used as an explanatory framework. It is shown that use of the central fund grew during the period from covering less than 1% of the University’s outputs to more than 12%. Health and Life Sciences disciplines made greatest use of the fund.

Although highly variable, average APC prices rose during the period, with fully OA publishers setting lower average APCs. APCs were paid largely from internal funds, but external funding became increasingly important. Key factors in adoption are identified to be increasing awareness and changing perceptions of OA, communication, disciplinary differences, and adoption mandates.

The study provides a detailed longitudinal analysis of one of the earliest central funds to be established globally with a theoretically informed explanatory model to inform future work on managing central funds and developing institutional and national OA policies.

URL : Researchers’ Adoption of an Institutional Central Fund for Open-Access Article-Processing Charges

DOI: 10.1177/2158244015625447

Large-Scale Analysis of the Accuracy of the Journal Classification Systems of Web of Science and Scopus

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Journal classification systems play an important role in bibliometric analyses. The two most important bibliographic databases, Web of Science and Scopus, each provide a journal classification system. However, no study has systematically investigated the accuracy of these classification systems. To examine and compare the accuracy of journal classification systems, we define two criteria on the basis of direct citation relations between journals and categories.

We use Criterion I to select journals that have weak connections with their assigned categories, and we use Criterion II to identify journals that are not assigned to categories with which they have strong connections. If a journal satisfies either of the two criteria, we conclude that its assignment to categories may be questionable. Accordingly, we identify all journals with questionable classifications in Web of Science and Scopus.

Furthermore, we perform a more in-depth analysis for the field of Library and Information Science to assess whether our proposed criteria are appropriate and whether they yield meaningful results. It turns out that according to our citation-based criteria Web of Science performs significantly better than Scopus in terms of the accuracy of its journal classification system.

URL : http://arxiv.org/abs/1511.00735

A review of the literature on citation impact indicators

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Citation impact indicators nowadays play an important role in research evaluation, and consequently these indicators have received a lot of attention in the bibliometric and scientometric literature. This paper provides an in-depth review of the literature on citation impact indicators. First, an overview is given of the literature on bibliographic databases that can be used to calculate citation impact indicators (Web of Science, Scopus, and Google Scholar).

Next, selected topics in the literature on citation impact indicators are reviewed in detail. The first topic is the selection of publications and citations to be included in the calculation of citation impact indicators. The second topic is the normalization of citation impact indicators, in particular normalization for field differences.

Counting methods for dealing with co-authored publications are the third topic, and citation impact indicators for journals are the last topic. The paper concludes by offering some recommendations for future research.

URL : http://arxiv.org/abs/1507.02099

Who Owns This Article? Applying Copyright’s Work-Made- for-Hire Doctrine to Librarians’ Scholarship

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The  Copyright  Act  of  1976  provides  that  works—including  scholarship—written within  the  scope  of  employment  belong  to  employers.  But  copyright  law  and  actual practices  widely  diverge.  The  academic  community  generally  allows  librarians  to  claim ownership of their writing, even when that ignores copyright law. Mr. Hellyer supports copyright ownership by librarians, and calls for the law and common practices to be harmonized.

URL : http://www.aallnet.org/mm/Publications/llj/LLJ-Archives/vol-108/no-1/2016-2.pdf