Wikidata as a semantic framework for the Gene Wiki initiative

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

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

How do scientists perceive the current publication culture? A qualitative focus group interview study among Dutch biomedical researchers

Design

Qualitative focus group interview study.

Setting

Four university medical centres in the Netherlands.

Participants

Three randomly selected groups of biomedical scientists (PhD, postdoctoral staff members and full professors).

Main outcome measures

Main themes for discussion were selected by participants.

Results

Frequently perceived detrimental effects of contemporary publication culture were the strong focus on citation measures (like the Journal Impact Factor and the H-index), gift and ghost authorships and the order of authors, the peer review process, competition, the funding system and publication bias. These themes were generally associated with detrimental and undesirable effects on publication practices and on the validity of reported results.

Furthermore, senior scientists tended to display a more cynical perception of the publication culture than their junior colleagues. However, even among the PhD students and the postdoctoral fellows, the sentiment was quite negative. Positive perceptions of specific features of contemporary scientific and publication culture were rare.

Conclusions

Our findings suggest that the current publication culture leads to negative sentiments, counterproductive stress levels and, most importantly, to questionable research practices among junior and senior biomedical scientists.

URL : How do scientists perceive the current publication culture? A qualitative focus group interview study among Dutch biomedical researchers

Alternative location : http://bmjopen.bmj.com/content/6/2/e008681.full

Reproducible Research Practices and Transparency across the Biomedical Literature

There is a growing movement to encourage reproducibility and transparency practices in the scientific community, including public access to raw data and protocols, the conduct of replication studies, systematic integration of evidence in systematic reviews, and the documentation of funding and potential conflicts of interest.

In this survey, we assessed the current status of reproducibility and transparency addressing these indicators in a random sample of 441 biomedical journal articles published in 2000–2014. Only one study provided a full protocol and none made all raw data directly available. Replication studies were rare (n = 4), and only 16 studies had their data included in a subsequent systematic review or meta-analysis. The majority of studies did not mention anything about funding or conflicts of interest.

The percentage of articles with no statement of conflict decreased substantially between 2000 and 2014 (94.4% in 2000 to 34.6% in 2014); the percentage of articles reporting statements of conflicts (0% in 2000, 15.4% in 2014) or no conflicts (5.6% in 2000, 50.0% in 2014) increased.

Articles published in journals in the clinical medicine category versus other fields were almost twice as likely to not include any information on funding and to have private funding. This study provides baseline data to compare future progress in improving these indicators in the scientific literature.

URL : Reproducible Research Practices and Transparency across the Biomedical Literature

DOI : 10.1371/journal.pbio.1002333

Views of Ethical Best Practices in Sharing Individual-Level Data From Medical and Public Health Research : A Systematic Scoping Review

There is increasing support for sharing individual-level data generated by medical and public health research. This scoping review of empirical research and conceptual literature examined stakeholders’ perspectives of ethical best practices in data sharing, particularly in low- and middle-income settings. Sixty-nine empirical and conceptual articles were reviewed, of which, only five were empirical studies and eight were conceptual articles focusing on low- and middle-income settings.

We conclude that support for sharing individual-level data is contingent on the development and implementation of international and local policies and processes to support ethical best practices. Further conceptual and empirical research is needed to ensure data sharing policies and processes in low- and middle-income settings are appropriately informed by stakeholders’ perspectives.

URL : Views of Ethical Best Practices in Sharing Individual-Level Data From Medical and Public Health Research

Alternative location : http://m.jre.sagepub.com/content/10/3/225

Sharing Public Health Research Data: Toward the Development of Ethical Data-Sharing Practice in Low- and Middle-Income Settings

It is increasingly recognized that effective and appropriate data sharing requires the development of models of good datasharing practice capable of taking seriously both the potential benefits to be gained and the importance of ensuring that the rights and interests of participants are respected and that risk of harms is minimized. Calls for the greater sharing of individual-level data from biomedical and public health research are receiving support among researchers and research funders. Despite its potential importance, data sharing presents important ethical, social, and institutional challenges in low-income settings.

In this article, we report on qualitative research conducted in five low- and middle-income countries exploring the experiences of key research stakeholders and their views about what constitutes good data-sharing practice.

URL : Sharing Public Health Research Data

Alternative location : http://m.jre.sagepub.com/content/10/3/217