The current status of Open Access in biomedical field: the comparison of countries relating to the impact of national policies

The purpose of the article is to show the current status of Open Access (OA) in biomedical field, and compare some countries such as the U.S., the U.K. and Japan in terms of the OA situation. There are controversies about the definition of OA. After examining the requirements about OA, we recognized OA as the situation in which researchers could read the full text of articles in unrestricted way. In order to investigate the current situation of OA, 4,756 articles were sampled randomly from articles published between January and September in 2005 and indexed in PubMed. The main results are as follows: 1) The rate of OA articles was 25%, and 75% of all the articles were available online including electronic subscription journal articles. 2) The means of OA was classified into five types. Among them, the rate of OA articles by “OA and Hybrid OA journals” was overwhelming (more than 70%), and that of PMC was 26.2%. The rates of OA articles by “institutional repositories” and “authors’ personal sites” were considerably low (6.0% and 4.9% respectively). 3) When comparing the rates of OA articles by countries, Belgium ranked the first with 41.7%. The five countries indicated more than 30% in OA articles: Canada and India (38.7%), Brazil (36.4%), Australia (30.8%), and the U.S. (30.7%). Each country was different in the means of OA. 4) We explored the rates of OA for two groups; one group consists of articles published in journals with an impact factor (IF), and the other consists of articles published in journals without IF. The rate of OA for the group of articles in journals with IF is 20.6%, and that of articles in journals without IF is 30.8%

Current status of open access in biomedical field-the comparison of countries related to the impact of national policies

The purpose of the article is to show the current status of Open Access (OA) in biomedical field, and compare some countries such as the U.S., the U.K. and Japan in terms of the OA situation. There are controversies about the definition of OA. After examining the requirements about OA, we recognized OA as the situation in which researchers could read the full text of articles in unrestricted way. In order to investigate the current situation of OA, 4,756 articles were sampled randomly from articles published between January and September in 2005 and indexed in PubMed. The main results are as follows: 1) The rate of OA articles was 25%, and 75% of all the articles were available online including electronic subscription journal articles. 2) The means of OA was classified into five types. Among them, the rate of OA articles by “OA and Hybrid OA journals” was overwhelming (more than 70%), and that of PMC was 26.2%. The rates of OA articles by “institutional repositories” and “authors’ personal sites” were considerably low (6.0% and 4.9% respectively). 3) When comparing the rates of OA articles by countries, Belgium ranked the first with 41.7%. The five countries indicated more than 30% in OA articles: Canada and India (38.7%), Brazil (36.4%), Australia (30.8%), and the U.S. (30.7%). Each country was different in the means of OA. 4) We explored the rates of OA for two groups; one group consists of articles published in journals with IF, and the other consists of articles published in journals without IF. The rate of OA for the group of articles in journals with IF is 20.6%, and that of articles in journals without IF is 30.8%

Remarkable growth of open access in the biomedical field: analysis of PubMed articles from 2006 to 2010.

INTRODUCTION: This study clarifies the trends observed in open access (OA) in the biomedical field between 2006 and 2010, and explores the possible explanations for the differences in OA rates revealed in recent surveys. METHODS: The study consists of a main survey and two supplementary surveys. In the main survey, a manual Google search was performed to investigate whether full-text versions of articles from PubMed were freely available. Target samples were articles published in 2005, 2007, and 2009; the searches were performed a year after publication in 2006, 2008, and 2010, respectively. Using the search results, we classified the OA provision methods into seven categories. The supplementary surveys calculated the OA rate using two search functions on PubMed: "LinkOut" and "Limits." RESULTS: The main survey concluded that the OA rate increased significantly between 2006 and 2010: the OA rate in 2010 (50.2%) was twice that in 2006 (26.3%). Furthermore, majority of OA articles were available from OA journal (OAJ) websites, indicating that OAJs have consistently been a significant contributor to OA throughout the period. OA availability through the PubMed Central (PMC) repository also increased significantly. OA rates obtained from two supplementary surveys were lower than those found in the main survey. "LinkOut" could find only 40% of OA articles in the main survey. DISCUSSION: OA articles in the biomedical field have more than a 50% share. OA has been achieved through OAJs. The reason why the OA rates in our surveys are different from those in recent surveys seems to be the difference in sampling methods and verification procedures

Number of sample articles for each survey.

<p>Number of sample articles for each survey.</p

Transitionin OA provision methods.^*

<p>* Because multiple OA sources for each article were counted, the percentages for each year add up to more than 100%.</p

Comparison of OA rates obtained by supplementary surveys and the main survey.

<p>PRF: Pls confirm that vertically merged cells and diagonal lines are correctly formatted.</p

Rising percentage of OA.

<p>Rising percentage of OA.</p

AKANE System: Protein-Protein Interaction 1 AKANE System: Protein-Protein Interaction Pairs in the BioCreAtIvE2 Challenge, PPI-IPS subtask

This report summarizes the participation of the Tsujii-lab group in the 2006 BioCreative2 text mining challenge 1. It describes the systems used, the results attained, and the lessons learned. The basic idea was to see how well the AKANE system could perform on a full-text Protein-Protein Interaction (PPI) Information Extraction (IE) task. AKANE system is a recently developed, sentence-level PPI system that achieved a 57.3 F-score on the AImed corpus. In order to use the AKANE system for the BioCreative task, the given training data had to be preprocessed. The BioCreative training data contained just a list of interacting protein pair identifiers for each given full-text article, while the expected input for the AKANE system is annotated sentences like in the AImed corpus. In order to transform the full-text articles into AImed sentence-level annotations, the text was first stripped of all HTML coding to get a plain text representation. Then, each mention of protein names were tagged by a Named Entity Recognizer (NER), and all interacting and co-occurring pairs in single sentences were used for training. A pipeline architecture was made to deal with each of these challenges. Some postprocessing was also necessary, in order to transform the results from the AKANE system into the expected format for the BioCreative2 challenge. The postprocessing included filtering and ranking the results, and balancing precision and recall to maximize the F-score

A de novo TOP2B variant associated with global developmental delay and autism spectrum disorder

Abstract Background TOP2B encodes type II topoisomerase beta, which controls topological changes during DNA transcription. TOP2B is expressed in the developing nervous system and is involved in brain development and neural differentiation. Recently, a de novo missense TOP2B variant (c.187C>T) has been identified in an individual with neurodevelopmental disorder (NDD). However, the association between TOP2B variants and NDDs remains uncertain. Methods Trio‐based whole‐exome sequencing was performed on a 7‐year‐old girl, presenting muscle hypotonia, stereotypic hand movements, epilepsy, global developmental delay, and autism spectrum disorder. Brain magnetic resonance images were normal. She was unable to walk independently and spoke no meaningful words. Results We found a de novo variant in TOP2B (NM_001330700.1:c.187C>T, p.(His63Tyr)), which is identical to the previous case. The clinical features of the two individuals with the c.187C>T variant overlapped. Conclusion Our study supports the finding that TOP2B variants may cause NDDs