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http://www-pmr.ch.cam.ac.uk/wiki/Oscar3
OSCAR is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries. This tool for shallow, chemistry-specific parsing of chemical documents identifies (or attempts to identify): * Chemical names: singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names. * Ontology terms: if you can do it by string-matching, you can get OSCAR to do it. * Chemical data: Spectra, melting/boiling point, yield etc. in experimental sections. In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing (OPSIN), and with identifiers from the chemical ontology ChEBI Current work on OSCAR3 by Peter Corbett focuses on its use in SciBorg, a framework for the deep parsing of chemical text. OSCAR3 also includes the Oscar Server, a Jetty-powered set of servlets. These provide the following services: * Parsing of text/HTML by OSCAR. * Text/InChI/SMILES/SMILES substructues/SMILES similarity search of papers, coupled with keyword and ontology-based search, using Lucene and the CDK. * List of all names found / all names that co-occur with a search term or terms. * Online management of a chemical/stopword lexicon. * Manual editing of SciXML fragments containing named entities, for creating of gold standards and training data. Oscar3 can be found on SourceForge: http://sourceforge.net/projects/oscar3-chem/
Proper citation: Oscar3 (RRID:SCR_004561) Copy
http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS/
Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOrt-ITEMS (RRID:SCR_004716) Copy
Located in the city of Galway in Ireland.
Proper citation: National University of Ireland; Galway; Ireland (RRID:SCR_004677) Copy
A multiple-sample, technology-aware SNP and indel caller.
Proper citation: UnifiedGenotyper (RRID:SCR_004710) Copy
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075146
An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations.
Proper citation: NuChart (RRID:SCR_004703) Copy
https://bams1.org/ontology/viewer.php
Ontology designed for neuroscience. Includes complete set of concepts that describe parts of rat nervous system, growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts.
Proper citation: BAMS Neuroanatomical Ontology (RRID:SCR_004616) Copy
http://matsen.fhcrc.org/pplacer/
Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
Proper citation: Pplacer (RRID:SCR_004737) Copy
Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences.
Proper citation: TETRA (RRID:SCR_004573) Copy
Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.
Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy
http://purl.bioontology.org/ontology/JERM
An ontology to describe the entities and relationships in the SEEK database, a Systems Biology environment for the sharing and exchange of data and models. The SysMO-SEEK database contains the work of the SysMO consortium (Systems Biology of Micro-Organisms) https://seek.sysmo-db.org/
Proper citation: SysMO JERM Ontology of Systems Biology for Micro-Organisms (RRID:SCR_004569) Copy
Network evaluating consensus-based common data elements (CDE) for traumatic brain injury (TBI) and psychological health (TBI-CDE, www.commondataelements.ninds.nih.gov/TBI.aspx) while extensively phenotyping a cohort of TBI patients across the injury spectrum from concussion to coma. Institutions that participate in the TBI Network will be able to track the outcomes of patients through a 3, 6 and 12-month followup program and compare outcomes with other participating institutions. For the three acute care centers, patients were enrolled that presented to the emergency department within 24 hours of head injury and required computed tomography (CT). For the rehabilitation center, referrals from acute hospitals were enrolled. Patients were consented to participate in components: clinical profile; blood draws for measurement of proteomic and genomic markers; 3T MRI within 2 weeks; three-month Glasgow Outcome Scale-Extended (GOS-E); and six-month TBI-CDE Core outcome assessments. A web-enabled database, imaging repository, and biospecimen bank was developed using the TBI-CDE recommendations. A total of 605 patients were enrolled. Of these subjects, 88% had a GCS 13-15, 5% had a GCS 9-12, and 7% had a GCS of 8 or less. Three-month GOS-E''s were obtained for 78% of the patients. Comprehensive 6-month outcome measures, including PTSD assessment, are ongoing until September 2011. Blood specimens were collected from 450 patients. Initial CTs for 605 patients and 235 patients with 3T MRI studies were transferred to an imaging repository. The TRACK TBI Network will provide qualified institutions access to a web-based version of key forms in tracking TBI outcomes for Quality Improvement and institutional benchmarking.
Proper citation: TRACK TBI Network (RRID:SCR_004723) Copy
UKM affirms integration of faith in Allah and constructive knowledge along with amalgamation of theory and practice as core fundamentals in advancement of knowledge, building of educated society and development of university.
Proper citation: National University of Malaysia; Selangor; Malaysia (RRID:SCR_004724) Copy
http://www.researchgate.net/jobs/research/
Job board for science professionals worldwide. You may search through international listings in science and research or post your job listing for free. Advanced filters are available and you may also research jobs by field. Currently, fields include: Agricultural Science, Anthropology, Biology, Chemistry, Computer Science, Design, Economics, Education, Engineering, Entertainment and Arts, Geoscience, History, Law, Linguistics, Literature, Mathematics, Medicine, Other, Philosophy, Physics, Political Science, Psychology, Religious Studies, Social Science, Space Science
Proper citation: ResearchGate: Research Jobs (RRID:SCR_004641) Copy
https://sites.google.com/a/lbl.gov/biopig/
Software providing a framework for genomic data analysis using Apache Pig and Hadoop.
Proper citation: BioPig (RRID:SCR_004636) Copy
Drug discovery company providing pharma with protein and antibody therapeutics in the fields of Oncology and Immunology.
Proper citation: Compugen (RRID:SCR_004631) Copy
An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels.
Proper citation: Jackson Laboratory (RRID:SCR_004633) Copy
Research university in Hsinchu City, Taiwan. Public institution that traces its roots back to 1911, when it was established in Beijing as Tsing Hua Academy.
Proper citation: National Tsing Hua University; Hsinchu; Taiwan (RRID:SCR_004590) Copy
https://github.com/lmrodriguezr/nonpareil
Estimate average coverage and create Nonpareil curves for metagenomic datasets.
Proper citation: Nonpareil (RRID:SCR_004629) Copy
http://www.hema-quebec.qc.ca/index.en.html
Hema-Quebec''s mission is to efficiently provide adequate quantities of safe, optimal blood components, substitutes, human tissues and cord blood to meet the needs of all Quebecers; provide and develop expertise along with specialized and innovative services and products in the fields of transfusion medicine and human tissue transplantation. Hema-Quebec is driven by the commitment, support and recognition of its employees as well as the trust of its partners to remain the standard of quality and innovation with respect to the safe procurement of blood products, human tissues and stem cells.
Proper citation: Hema-Quebec (RRID:SCR_004700) Copy
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