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Literature DB >> 31702580

Automatic annotation of protein residues in published papers.

Robert Firth¹, Francesco Talo², Aravind Venkatesan², Abhik Mukhopadhyay², Johanna McEntyre², Sameer Velankar², Chris Morris¹.

Abstract

This work presents an annotation tool that automatically locates mentions of particular amino-acid residues in published papers and identifies the protein concerned. These matches can be provided in context or in a searchable format in order for researchers to better use the existing and future literature.

Keywords: NLP; named entity recognizer; natural language processing; residue

Mesh：

Substances：
Amino Acids
Proteins

Year: 2019 PMID： 31702580 PMCID： PMC6839820 DOI： 10.1107/S2053230X1901210X

Source DB: PubMed Journal: Acta Crystallogr F Struct Biol Commun ISSN： 2053-230X Impact factor: 1.056

10 in total

1. Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors.

Authors: Florence Horn; Anthony L Lau; Fred E Cohen
Journal: Bioinformatics Date: 2004-01-22 Impact factor: 6.937

2. Disruption of cytoplasmic and mitochondrial folylpolyglutamate synthetase activity in Saccharomyces cerevisiae.

Authors: L DeSouza; Y Shen; A L Bognar
Journal: Arch Biochem Biophys Date: 2000-04-15 Impact factor: 4.013

3. Pseudomonas aeruginosa possesses homologues of mammalian phenylalanine hydroxylase and 4 alpha-carbinolamine dehydratase/DCoH as part of a three-component gene cluster.

Authors: G Zhao; T Xia; J Song; R A Jensen
Journal: Proc Natl Acad Sci U S A Date: 1994-02-15 Impact factor: 11.205

4. Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens.

Authors: Armelle Vigouroux; Abbas El Sahili; Julien Lang; Magali Aumont-Nicaise; Yves Dessaux; Denis Faure; Solange Moréra
Journal: Sci Rep Date: 2017-12-21 Impact factor: 4.379

5. SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data.

Authors: Aravind Venkatesan; Jee-Hyub Kim; Francesco Talo; Michele Ide-Smith; Julien Gobeill; Jacob Carter; Riza Batista-Navarro; Sophia Ananiadou; Patrick Ruch; Johanna McEntyre
Journal: Wellcome Open Res Date: 2017-07-10

6. nala: text mining natural language mutation mentions.

Authors: Juan Miguel Cejuela; Aleksandar Bojchevski; Carsten Uhlig; Rustem Bekmukhametov; Sanjeev Kumar Karn; Shpend Mahmuti; Ashish Baghudana; Ankit Dubey; Venkata P Satagopam; Burkhard Rost
Journal: Bioinformatics Date: 2017-06-15 Impact factor: 6.937

1 in total

1. Taking biological structure communications into the third dimension.

Authors: Mark J van Raaij; Janet Newman
Journal: Acta Crystallogr F Struct Biol Commun Date: 2019-11-05 Impact factor: 1.056

1 in total

Automatic annotation of protein residues in published papers.

1. Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors.

2. Disruption of cytoplasmic and mitochondrial folylpolyglutamate synthetase activity in Saccharomyces cerevisiae.

3. Pseudomonas aeruginosa possesses homologues of mammalian phenylalanine hydroxylase and 4 alpha-carbinolamine dehydratase/DCoH as part of a three-component gene cluster.

4. Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens.

5. SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data.

6. nala: text mining natural language mutation mentions.

7. Kinetic and Structural Characterization of the Effects of Membrane on the Complex of Cytochrome b ₅ and Cytochrome c.

8. UniProt: the universal protein knowledgebase.

9. Reuse of terminological resources for efficient ontological engineering in Life Sciences.

10. Literature mining of protein-residue associations with graph rules learned through distant supervision.

1. Taking biological structure communications into the third dimension.