Vita, Randi Zheng, Jie Jackson, Rebecca Dooley, Damion Overton, James A Miller, Mark A Berrios, Daniel C Scheuermann, Richard H He, Yongqun McGinty, Hande Küçük
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Published in
Database : the journal of biological databases and curation
The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized temp...
Burns, Gully A Li, Xiangci Peng, Nanyun
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Database
We investigate the application of deep learning to biocuration tasks that involve classification of text associated with biomedical evidence in primary research articles. We developed a large-scale corpus of molecular papers derived from PubMed and PubMed Central open access records and used it to train deep learning word embeddings under the GloVe...
Rey, Julien Deschavanne, Patrick Pierre Tuffery
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Database
With the recent progress in complete genome sequencing, mining the increasing amount of genomic information available should in theory provide the means to discover new classes of peptides. However, annotation pipelines often do not consider small reading frames likely to be expressed. BactPepDB, available online at http://bactpepdb.rpbs.univ-paris...
Wiley, Laura K Sivley, R Michael Bush, William S
Published in
Database : the journal of biological databases and curation
Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the development of stand-alone applicatio...
Liechti, R Csardi, G Bergmann, S Schuetz, F Sengstag, T Boj, SF Servitja, J-M Ferrer, J Van Lommel, L Schuit, F
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Type 2 diabetes mellitus (T2DM) is a major disease affecting nearly 280 million people worldwide. Whilst the pathophysiological mechanisms leading to disease are poorly understood, dysfunction of the insulin-producing pancreatic beta-cells is key event for disease development. Monitoring the gene expression profiles of pancreatic beta-cells under s...
Van Camp, Ann J
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Database
Wilks, C Cline, Ms Weiler, E Diehkans, M Craft, B Martin, C Murphy, D Pierce, H Black, J Nelson, D
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Published in
Database
The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. ...
Wilks, C Cline, Ms Weiler, E Diehkans, M Craft, B Martin, C Murphy, D Pierce, H Black, J Nelson, D
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Published in
Database
The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. ...
Wilks, C Cline, Ms Weiler, E Diehkans, M Craft, B Martin, C Murphy, D Pierce, H Black, J Nelson, D
...
Published in
Database
The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. ...
Wilks, C Cline, Ms Weiler, E Diehkans, M Craft, B Martin, C Murphy, D Pierce, H Black, J Nelson, D
...
Published in
Database
The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. ...
