39 research outputs found

    Large expert-curated database for benchmarking document similarity detection in biomedical literature search

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    Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

    The sugarcane signal transduction (SUCAST) catalogue: prospecting signal transduction in sugarcane

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    EST sequencing has enabled the discovery of many new genes in a vast array of organisms, and the utility of this approach to the scientific community is greatly increased by the establishment of fully annotated databases. The present study aimed to identify sugarcane ESTs sequenced in the sugarcane expressed sequence tag (SUCEST) project (<A HREF="http://sucest.lad.ic.unicamp.br/">http://sucest.lad.ic.unicamp.br</A>) that corresponded to signal transduction components. We also produced a sugarcane signal transduction (SUCAST) catalogue (<A HREF="http://sucest.lad.ic.unicamp.br/private/mining-reports/QG/QG-mining.htm">http://sucest.lad.ic.unicamp.br/private/mining-reports/QG/QG-mining.htm</A>) that covered the main categories and pathways. Expressed sequence tags (ESTs) encoding enzymes for hormone (gibberellins, ethylene, auxins, abscisic acid and jasmonic acid) biosynthetic pathways were found and tissue specificity was inferred from their relative frequency of occurrence in the different libraries. Whenever possible, transducers of hormones and plant peptide signaling were catalogued to the respective pathway. Over 100 receptors were found in sugarcane, which contains a large family of Ser/Thr kinase receptors and also photoreceptors, histidine kinase receptors and their response regulators. G-protein and small GTPases were analyzed and compared to known members of these families found in mammalian and plant systems. Major kinase and phosphatase pathways were mapped, with special attention being given to the MAP kinase and the inositol pathway, both of which are well known in plants.<br>O sequenciamento de ESTs (etiquetas de sequencias transcritas) tem possibilitado a descoberta de muitos novos genes em uma ampla variedade de organismos. Um aumento do aproveitamento desta informação pela comunidade científica tem sido possível graças ao desenvolvimento de base de dados contendo seqüências completamente anotadas. O trabalho aqui relatado teve como objetivo a identificação de ESTs de cana de açúcar seqüenciadas através do projeto SUCEST (<A HREF="http://sucest.lad.ic.%20unicamp.br/">http://sucest.lad.ic. unicamp.br</A>) que codificam para proteínas envolvidas em mecanismos de transdução de sinal. Nós também preparamos um catálogo dos componentes de transdução de sinal da cana de açúcar (SUCAST) englobando as principais categorias e vias conhecidas (<A HREF="http://sucest.lad.ic.unicamp.%20br/private/mining-reports/QG/QG-mining.htm">http://sucest.lad.ic.unicamp. br/private/mining-reports/QG/QG-mining.htm</A>). ESTs codificadoras de enzimas envolvidas nas rotas de biossíntese de hormônios (giberelinas, etileno, auxinas, ácido abscíssico, ácido jasmônico) foram encontradas e sua expressão específica nos tecidos foi inferida a partir de seu enriquecimento nas diferentes bibliotecas. Quando possível, transmissores do sinal hormonal e da resposta a peptídeos produzidos pela planta foram associados a suas respectivas vias. Mais de 100 receptores foram encontrados na cana de açúcar, entre os quais uma grande família de receptores Ser/Thr quinase e também de fotoreceptores, receptores do tipo histidina quinase e seus respectivos reguladores da resposta. Proteínas G e GTPases pequenas foram também analisadas e comparadas com membros destas famílias já conhecidos em mamíferos e plantas. As vias principais que envolvem a participação de proteínas quinases e fosfatases foram mapeadas, em especial as vias da quinase MAP quinase e do inositol que são bem estudadas em plantas
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