Experiences in Automatic Keywording of Particle Physics Literature

Attributing keywords can assist in the classification and retrieval of documents in the particle physics literature. As information services face a future with less available manpower and more and more documents being written, the possibility of keyword attribution being assisted by automatic classification software is explored. A project being carried out at CERN (the European Laboratory for Particle Physics) for the development and integration of automatic keywording is described

Experiences in Automatic Keywording of Particle Physics Literature

Attributing keywords can assist in the classification and retrieval of documents in the particle physics literature. As information services face a future with less available manpower and more and more documents being written, the possibility of keyword attribution being assisted by automatic classification software is explored. A project being carried out at CERN (the European Laboratory for Particle Physics) for the development and integration of automatic keywording is described

Automatic keywording of High Energy Physics

Bibliographic databases were developed from the traditional library card catalogue in order to enable users to access library documents via various types of bibliographic information, such as title, author, series or conference date. In addition these catalogues sometimes contained some form of indexation by subject, such as the Universal (or Dewey) Decimal Classification used for books. With the introduction of the eprint archives, set up by the High Energy Physics (HEP) Community in the early 90s, huge collections of documents in several fields have been made available on the World Wide Web. These developments however have not yet been followed up from a keywording point of view. We will see in this paper how important it is to attribute keywords to all documents in the area of HEP Grey Literature. As libraries are facing a future with less and less manpower available and more and more documents, we will explore the possibility of being helped by automatic classification software. We will specifically mention a project being carried out at CERN (European Laboratory for Particle Physics) for testing this automatic keywording

Quantitative Analysis of the Publishing Landscape in High-Energy Physics

World-wide collaboration in high-energy physics (HEP) is a tradition which dates back several decades, with scientific publications mostly coauthored by scientists from different countries. This coauthorship phenomenon makes it difficult to identify precisely the ``share'' of each country in HEP scientific production. One year's worth of HEP scientific articles published in peer-reviewed journals is analysed and their authors are uniquely assigned to countries. This method allows the first correct estimation on a ``pro rata'' basis of the share of HEP scientific publishing among several countries and institutions. The results provide an interesting insight into the geographical collaborative patterns of the HEP community. The HEP publishing landscape is further analysed to provide information on the journals favoured by the HEP community and on the geographical variation of their author bases. These results provide quantitative input to the ongoing debate on the possible transition of HEP publishing to an Open Access model.Comment: For a better on-screen viewing experience this paper can also be obtained at: http://doc.cern.ch/archive/electronic/cern/preprints/open/open-2006-065.pd

Patchy promiscuity:machine learning applied to predict the host specificity of <i>Salmonella enterica </i>and <i>Escherichia coli</i>

Supporting data for Patchy promiscuity: machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli, as published in <em>Microbial Genomics</em

Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157:H7 in the UK

Over the last 35 years in the UK, the burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods of time, been associated with five different sub-lineages (1983-1995, Ia, I/IIa and I/IIb; 1996-2014, Ic; and 2015-2018, IIb). The acquisition of a stx2a-encoding bacteriophage by these five sub-lineages appears to have coincided with their respective emergences. The Oxford Nanopore Technologies (ONT) system was used to sequence, characterize and compare the stx-encoding prophages harboured by each sub-lineage to investigate the integration of this key virulence factor. The stx2a-encoding prophages from each of the lineages causing clinical disease in the UK were all different, including the two UK sub-lineages (Ia and I/IIa) circulating concurrently and causing severe disease in the early 1980s. Comparisons between the stx2a-encoding prophage in sub-lineages I/IIb and IIb revealed similarity to the prophage commonly found to encode stx2c, and the same site of bacteriophage integration (sbcB) as stx2c-encoding prophage. These data suggest independent acquisition of previously unobserved stx2a-encoding phage is more likely to have contributed to the emergence of STEC O157:H7 sub-lineages in the UK than intra-UK lineage to lineage phage transmission. In contrast, the stx2c-encoding prophage showed a high level of similarity across lineages and time, consistent with the model of stx2c being present in the common ancestor to extant STEC O157:H7 and maintained by vertical inheritance in the majority of the population. Studying the nature of the stx-encoding bacteriophage contributes to our understanding of the emergence of highly pathogenic strains of STEC O157:H7

Establishing a consortium for Open Access (OA) publishing in particle physics

A meeting has been called at CERN on November 3rd 2006 to work towards establishing a consortium of major particle physics funding agencies, aimed at guiding a transition of the current subscription model for journals to a more stable, more competitive and more affordable future for the dissemination of quality-assured scientific information adapted to the era of electronic publishing. The meeting will gather representatives of major European particle physics agencies and library consortia. In order to be successful it is vital that the stakeholders, representing as they do the funding bodies and academia, see themselves responsible for the financing and organization of the dissemination of scientific information and its quality assurance. In particular the transition to a wider availability of research results cannot afford to be held back due to a lack of concerted effort among the agencies financing the research