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LINNAEUS specifications

Information


Unique identifier OMICS_09123
Name LINNAEUS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Casey M. Bergman <>

Publication for LINNAEUS

LINNAEUS in pipelines

 (3)
2017
PMCID: 5737205
PMID: 29220457
DOI: 10.1093/database/bax062

[…] the query expansion & modification module., first, as illustrated in , this module processes the query in parallel with four sub-components, category identification, dnorm (), gennorm () and linnaeus (). the category identification tools identifies what type of data are targeted by the query, and the other tools tag mentions of biological entities including diseases, genes and organisms […]

2017
PMCID: 5737205
PMID: 29220457
DOI: 10.1093/database/bax062

[…] in the previous subsection gave us the intuition that led us to propose our strategy for a multi-field query builder. recall that the query is processed by three sub-components, dnorm, gennorm and linnaeus, which, respectively, identify diseases, genes and organisms mentioned in the query. once done, a new query is built as follows: the title, description and article title fields are always […]

2013
PMCID: 3662864
PMID: 23707966
DOI: 10.1093/database/bat033

[…] researchers to explore these trends in relation to interactions, we matched disease terms from an in-house disease lexicon (containing 4861 terms with 205 373 case-sensitive synonyms) to p1 using linnaeus (). we then adopted the same method used in the pain relevancy scoring to calculate the relevancy of each event chain to each disease term match and from these the overall disease relevancy […]


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LINNAEUS in publications

 (16)
PMCID: 5558737
PMID: 28810903
DOI: 10.1186/s12859-017-1776-8

[…] previously used for sequential labeling tasks of the form we consider here. for these reasons, in the following comparison we focus on the remaining corpora: anatem, bc2gm, bc4chemd, bc5cdr, jnlpba, linnaeus, and ncbi-disease., the anatem corpus was created for anatomical entity mention recognition and released with a benchmark system, anatomytagger, which scored 91.61% f-score for right […]

PMCID: 5393592
PMID: 28414821
DOI: 10.1371/journal.pone.0175277

[…] of its authority fields (i.e., the name of the first person to publish it and the year that it was coined), which can be written in different formats. for example, biologists can use panthera leo (linnaeus, 1758), panthera leo linnaeus, 1758 or panthera leo linnaeus 1758 to refer to the same species. another challenge arises when biologists indicate genus or sub-genus by using only the initial […]

PMCID: 4962763
PMID: 27465130
DOI: 10.1093/database/baw111

[…] false negatives (fns). for example, the prefixes hsa and mmu in ‘(hsa)sema6a-1’ and ‘(mmu)sema6a-1’ indicate human and murine, respectively., comparison of the species recognition performance on the linnaeus and species-800 corpora. , in addition to the isn corpus, we evaluated the performance of the developed module on two other corpora annotated with species information. the first […]

PMCID: 4719073
PMID: 26420781
DOI: 10.1093/bib/bbv087

[…] new ways of referring to them). an open-source ner engine, banner [], with models to recognize genes and diseases mentioned in biomedical text, is currently available for gene and disease ner, and linnaeus is available for species []. rebholz-schuhmann et al. [] present an overview of the ner solutions for the second calbc task, including protein, disease, chemical (drug) and species entities. […]

PMCID: 4511510
PMID: 26202570
DOI: 10.1186/1471-2105-16-S10-S2

[…] complexes was available, we applied heuristics based on the gene or gene product annotation and dictionary-based tagging to create the initial annotations for the pc task complex type. finally, linnaeus [] was applied for the cg task organism mentions. the overall processing used the pipeline first introduced for similar analysis for the bionlp st'11 []. these tools were additionally […]


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LINNAEUS institution(s)
Faculty of Life Sciences, University of Manchester, Manchester, UK; School of Computer Science, University of Manchester, Manchester, UK

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