Open Access Metadata for Journals in Directory of Open Access Journals: Who, How, and What Scheme?

Open access (OA) is a form of publication that allows some level of free access to scholarly publications. The Directory of Open Access Journals (DOAJ) is a repository to which OA journals may apply and upload content to increase discoverability. OA also refers to metadata that is freely available for harvesting. In making metadata open access, standards for schemes and protocols are needed to facilitate interoperability. For open access journals, such as those listed in the DOAJ, providing open access metadata in a form that promotes interoperability is essential for discoverability of their content. This paper investigates what standards exist or are emerging, who within journals is creating the metadata for DOAJ journals, and how are those journals and DOAJ sharing the metadata for articles. Moreover, since creating metadata requires specialized knowledge of both librarians and programmers, it is imperative that journals wanting to publish with OA metadata formulate plans to coordinate these experts and to be sure their efforts are compatible with current standards and protocols

PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net

Survey over Existing Query and Transformation Languages

A widely acknowledged obstacle for realizing the vision of the Semantic Web is the inability of many current Semantic Web approaches to cope with data available in such diverging representation formalisms as XML, RDF, or Topic Maps. A common query language is the first step to allow transparent access to data in any of these formats. To further the understanding of the requirements and approaches proposed for query languages in the conventional as well as the Semantic Web, this report surveys a large number of query languages for accessing XML, RDF, or Topic Maps. This is the first systematic survey to consider query languages from all these areas. From the detailed survey of these query languages, a common classification scheme is derived that is useful for understanding and differentiating languages within and among all three areas

Bibliographic Control of Serial Publications

An important problem with serials is bibliographic control. What good does it do for libraries to select, acquire, record, catalog, and bind large holdings of serial publications if the contents of those serials remain a mystery to all except the few who have the opportunity to examine selected journals of continuing personal interest and have discovered some magic way of retaining the gist of the contents? Bibliographic control is the indexing and abstracting of the contents or guts of what is included in the serials. It is this control, provided by secondary publishing services, which this article will discuss. Just as there are problems with serials in general, there are some easily identifiable problems connected with their bibliographic control including: volume, overlap, costs, elements and methods, and a few other miscellaneous considerations. Some history of bibliographic control will also put the current problems in a helpful perspective. Hereafter "bibliographic control" will be designated by the term "abstracting and indexing," one of these alone, or the shorter "a & i." (I do distinguish between abstracting and indexing and believe that they are not in order of importance and difficulty.) Although a & i do provide bibliographic control, this paper will not discuss cataloging, tables of contents, back-of-the-book indexes, year-end indexes, cumulative indexes, lists of advertisers, or bibliographies. If there is to be control, there must always be indexing. Abstracting is a short cut, a convenience, and perhaps a bibliographic luxury which may be now, or is fast becoming, too rich, in light of other factors to be discussed, for library blood and for the users of libraries especially for the users of indexes who may not depend upon the library interface. Abstracting, though, provides a desirable control, and one which will continue to be advocated.published or submitted for publicatio