Special Libraries, Winter 1986

Volume 77, Issue 1https://scholarworks.sjsu.edu/sla_sl_1986/1000/thumbnail.jp

An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights

With an unprecedented growth in the biomedical literature, keeping up to date with the new developments presents an immense challenge. Publications are often studied in isolation of the established literature, with interpretation being subjective and often introducing human bias. With ontology-driven annotation of biomedical data gaining popularity in recent years and online databases offering metatags with rich textual information, it is now possible to automatically text-mine ontological terms and complement the laborious task of manual management, interpretation, and analysis of the accumulated literature with downstream statistical analysis. In this paper, we have formulated an automated workflow through which we have identified ontological information, including nutrition-related terms in PubMed abstracts (from 1991 to 2016) for two main types of Inflammatory Bowel Diseases: Crohn’s Disease and Ulcerative Colitis; and two other gastrointestinal (GI) diseases, namely, Coeliac Disease and Irritable Bowel Syndrome. Our analysis reveals unique clustering patterns as well as spatial and temporal trends inherent to the considered GI diseases in terms of literature that has been accumulated so far. Although automated interpretation cannot replace human judgement, the developed workflow shows promising results and can be a useful tool in systematic literature reviews. The workflow is available at https://github.com/KociOrges/pytag

The devices, experimental scaffolds, and biomaterials ontology (DEB): a tool for mapping, annotation, and analysis of biomaterials' data

The size and complexity of the biomaterials literature makes systematic data analysis an excruciating manual task. A practical solution is creating databases and information resources. Implant design and biomaterials research can greatly benefit from an open database for systematic data retrieval. Ontologies are pivotal to knowledge base creation, serving to represent and organize domain knowledge. To name but two examples, GO, the gene ontology, and CheBI, Chemical Entities of Biological Interest ontology and their associated databases are central resources to their respective research communities. The creation of the devices, experimental scaffolds, and biomaterials ontology (DEB), an open resource for organizing information about biomaterials, their design, manufacture, and biological testing, is described. It is developed using text analysis for identifying ontology terms from a biomaterials gold standard corpus, systematically curated to represent the domain's lexicon. Topics covered are validated by members of the biomaterials research community. The ontology may be used for searching terms, performing annotations for machine learning applications, standardized meta-data indexing, and other cross-disciplinary data exploitation. The input of the biomaterials community to this effort to create data-driven open-access research tools is encouraged and welcomed.Preprin

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Preliminary Report on Patent Literature, Search Methodology and Patent Status of Medicines on the WHO EML 2009

Over the past several decades the World Health Organization (WHO) has produced the Essential Medicines List (EML) to assist countries in deciding what medicines should be essential and available in National Essential Medicine Lists.1 WHO, through the work of regional offices, supports nations using the EML to ensure the quality, availability, and affordability of pharmaceuticals required to promote and advance public health in nations across the globe. However in some cases, access to EML pharmaceuticals might be complicated by existing patents, i.e., where issued, patent rights might pose obstacles to access and inclusion in national EMLs. Indeed, in developed and emerging economy national jurisdictions patent protection may be in effect for a not insignificant number of the WHO EML pharmaceuticals (Figure 2A). However, in developing countries, it is uncertain whether these patents have been filed or issued. Without patent data predicated on an established, reproducible protocol for accessing and assembling patent information on the EML pharmaceuticals, discussions, debates and strategic approaches to understanding and managing patents with regard to access and delivery to developing countries remain in the dark. Indeed, it is absurd to make policy and formulate strategy without solid patent information: the critical foundation for rational debate. To analyze the degree and scope of patenting of EML pharmaceuticals, WIPO (with WHO) approached the Franklin Pierce Center for Intellectual Property at the University of New Hampshire School of Law, specifically the International Technology Transfer Institute (ITTI) to generate a preliminary overview of patents appurtenant to recently added pharmaceutical updates to the EML.2 As part of this work, with inputs from WHO and WIPO, ITTI developed novel methodology and a detailed protocol for identifying EML pharmaceutical patents in national jurisdictions, with an easily reproducible yet cost effective template. Herein is described the development of such a protocol and a preliminary pool of patent information that illustrates its utility. The protocol yields data in a layered approach thereby allowing a user to quickly and effectively obtain both broad and detailed patent information for medications on the WHO EML. In addition, the protocol can be used as an initial path for targeted strategic analysis of potentially relevant patent information in national jurisdictions. In sum, the objectives for this project were: To develop a robust methodology to assess the patent status of medicines on the WHO Model List of Essential Medicines; To place in the public domain a detailed report on the present (2010) patent status of medicines that were on patent in 2003 and those medicines added to the Model List since 2003 by country and level of development; and To analyze the patent status of these Essential Medicines by the development status of countries. The report describes the development of the protocol and presents a preliminary list of EML and corresponding patents in certain jurisdictions to illustrate the utility of the approach. Results will be discussed both in terms of global access and patents, and in the context of establishing standard, systematic, protocols for periodic patent searches related to EML content. 1 WORLD HEALTH ORGANIZATION, CONTINUITY AND CHANGE IMPLEMENTING THE THIRD WHO MEDICINES STRATEGY 2008--‐2013 20 (WHO Press, 3rd ed. 2009). 2 This report covers the EML up to and including updates until 2009

Special Libraries, July 1980

Volume 71, Issue 7https://scholarworks.sjsu.edu/sla_sl_1980/1005/thumbnail.jp

Special Libraries, September 1978

Volume 69, Issue 9https://scholarworks.sjsu.edu/sla_sl_1978/1007/thumbnail.jp