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The Proteins API: accessing key integrated protein and genome information

Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin
2017 Nucleic Acids Research  
The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and  ...  The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing  ...  of Bioinformatics (SIB) and the Protein Information Resource (PIR).  ... 
doi:10.1093/nar/gkx237 pmid:28383659 pmcid:PMC5570157 fatcat:utre2jeq2vfl7gcmj3scf5pf5y

Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress

Èile Butler, Magnus Alsterfjord, Tobias C Olofsson, Christofer Karlsson, Johan Malmström, Alejandra Vásquez
2013 BMC Microbiology  
Results: The genomic analysis of the LAB demonstrated varying genome sizes ranging from 1.5 to 2.2 mega-base pairs (Mbps) which points out a clear difference within the protein gene content, as well as  ...  The most common known extra-cellular proteins secreted were enzymes, DNA chaperones, S-layer proteins, bacteriocins, and lysozymes.  ...  Per Håkansson's Foundation, and the Biotechnology and Biological Sciences Research Council's Insect Pollinators Initiative (grant BB/I000100/1).  ... 
doi:10.1186/1471-2180-13-235 pmid:24148670 pmcid:PMC4015849 fatcat:cyh46cl37vhora3vdvjlvffhdy

HCAtk and pyHCA: A Toolkit and Python API for the Hydrophobic Cluster Analysis of Protein Sequences [article]

Tristan Bitard-Feildel, Isabelle Callebaut
2018 bioRxiv   pre-print
The developed tools can be either used from command line or from a python API. Availability: HCAtk and pyHCA are available at https://github.com/T-B-F/pyHCA under the CeCILL-C license.  ...  Results: We developed pyHCA and HCAtk, a python API and standalone tool gathering together improved versions of previously developed methodologies, with new functionalities.  ...  Protein domain annotation 11 dominates analyses, describing a protein as a list of blocks corresponding to evolutionary and functional HCA toolkit (HCAtk), and its associated python API pyHCA.  ... 
doi:10.1101/249995 fatcat:546ly6bw35ccdnsye3iqmmgnb4

Proteomics analysis reveals protein expression differences for hypopharyngeal gland activity in the honeybee, Apis mellifera carnica Pollmann

Ting Ji, Zhenguo Liu, Jie Shen, Fang Shen, Qin Liang, Liming Wu, Guohong Chen, Miguel Corona
2014 BMC Genomics  
More than 10 key high-abundance proteins were involved in signaling pathways related to ribosome function and protein processing in the endoplasmic reticulum. The results were validated by qPCR.  ...  A total of 649 proteins were mapped to canonical signaling pathways found in the Kyoto Encyclopedia of Genes and Genomes (KEGG), which were preferentially associated with metabolism and biosynthesis of  ...  Dejun Ji, Ya'ni Zhang and Qi Xu in Yangzhou University for their advising on the revision.  ... 
doi:10.1186/1471-2164-15-665 pmid:25103401 pmcid:PMC4141115 fatcat:bj5g42biufe5zptttmdj72emwi

Transcriptome differences in the hypopharyngeal gland between Western Honeybees (Apis mellifera) and Eastern Honeybees (Apis cerana)

Hao Liu, Zi-Long Wang, Liu-Qing Tian, Qiu-Hong Qin, Xiao-Bo Wu, Wei-Yu Yan, Zhi-Jiang Zeng
2014 BMC Genomics  
Results: Twelve DGE-tag libraries were constructed and sequenced using the total RNA extracted from the HGs of newly emerged workers, nurses, and foragers of Apis mellifera and Apis cerana.  ...  Conclusions: In this study, we investigated the DEGs between the HGs of two sibling honeybee species (Apis mellifera and Apis cerana).  ...  Gui-Sheng Wu for helpful suggestions that improved the manuscript. This work was supported by the earmarked fund for China  ... 
doi:10.1186/1471-2164-15-744 pmid:25174638 pmcid:PMC4158095 fatcat:txdv7gpcongjpoujqyfgvm37qi

Reorganizing the protein space at the Universal Protein Resource (UniProt)

2011 Nucleic Acids Research  
The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with  ...  A key development at UniProt is the provision of complete, reference and representative proteomes.  ...  The UniProt Knowledgebase (UniProtKB) is an expertly curated database, a central access point for integrated protein information with cross-references to multiple sources.  ... 
doi:10.1093/nar/gkr981 pmid:22102590 pmcid:PMC3245120 fatcat:tpdi3er7yrdk7me7g3xmy6n3wy

NCBI's Virus Discovery Codeathon: Building "FIVE" —The Federated Index of Viral Experiments API Index

Joan Martí-Carreras, Alejandro Gener, Sierra Miller, Anderson Brito, Christiam Camacho, Ryan Connor, Ward Deboutte, Cody Glickman, David Kristensen, Wynn Meyer, Sejal Modha, Alexis Norris (+21 others)
2020 Viruses  
To this end, a Python API query system was developed to enhance the accessibility of FIVE.  ...  Many projects of database or index federation fail to provide easier alternatives to access or query information.  ...  to incorporate the protein domain-based information.  ... 
doi:10.3390/v12121424 pmid:33322070 pmcid:PMC7764237 fatcat:5bt5obp7wvau5ptgvjnxvdydem

Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross Overbeek, Veronika Vonstein, Rick Stevens, Robert A Edwards
2010 BMC Bioinformatics  
Acknowledgements Part of this project has been funded with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services  ...  We thank the beta-testers of this service especially Bahador Nosrat and Scott Kelley at San Diego State University. Author Details  ...  The API allows all users to access our systems, retrieve data, and develop tools for mining genomes and metagenomes essentially without restriction.  ... 
doi:10.1186/1471-2105-11-319 pmid:20546611 pmcid:PMC2900279 fatcat:pdhqjcy2ljhg5ac46xn6i4vmfy

Web scraping technologies in an API world

Daniel Glez-Peña, Anália Lourenço, Hugo López-Fernández, Miguel Reboiro-Jato, Florentino Fdez-Riverola
2013 Briefings in Bioinformatics  
Web services are the de facto standard in biomedical data integration. However, there are data integration scenarios that cannot be fully covered by Web services.  ...  Moreover, we describe the operation of WhichGenes and PathJam, two bioinformatics meta-servers that use scraping as means to cope with gene set enrichment analysis.  ...  Key Points Web services or API access are not always available in online biomedical resources.  ... 
doi:10.1093/bib/bbt026 pmid:23632294 fatcat:pzafuhg4wjdejlfomltdnopyxm

UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee (+122 others)
2020 Nucleic Acids Research  
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information.  ...  We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries.  ...  ACKNOWLEDGEMENTS The UniProt publication has been prepared by Alex Bateman, Maria  ... 
doi:10.1093/nar/gkaa1100 pmid:33237286 pmcid:PMC7778908 fatcat:6rwvp6l5uzb3li4lygf2gny6qq

UniProt: the universal protein knowledgebase

2016 Nucleic Acids Research  
To help interpretation of genomic variants, we provide tracks of detailed protein information for the major genome browsers.  ...  The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation.  ...  Mapping the UniProt human proteome to the reference genome With the increasing interest and progress in genomic-based medicine understanding the effects of variation on protein function is a key component  ... 
doi:10.1093/nar/gkw1099 pmid:27899622 pmcid:PMC5210571 fatcat:hk7eqzbncray5nfbzsehqikjnm

A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues

Queenie WT Chan, Robert Parker, Zhi Sun, Eric W Deutsch, Leonard J Foster
2011 BMC Genomics  
This publicly accessible and interactive database is an important framework for the current and future analysis of mass spectrometry data.  ...  The lack of a consolidated platform to organize this massive resource hampers our ability, and that of others, to mine the information to its maximum potential.  ...  ZS processed the raw data to generate the Honey Bee PeptideAtlas. QWTC, EWD and LJF wrote the initial version of the manuscript. All authors have read and approved the final manuscript.  ... 
doi:10.1186/1471-2164-12-290 pmid:21639908 pmcid:PMC3213019 fatcat:loimowhryfb3xcfliidp7zailq

Definition of data models and APIs

Karl Presser, Mark Roe, Agnieszka Matuszczak, Paul Finglas
2021 Zenodo  
Existing data standards, thesauri and APIs that can form the basis of data exchange in FNS-Cloud are evaluated.  ...  This deliverable reviews andprovides a map of food data areas relevant to FNS-Cloud and, for each data area, recommends a data exchange model, thesauri, and APIs.  ...  The UMLS integrates and distributes key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems  ... 
doi:10.5281/zenodo.6965954 fatcat:texctyfywzbhhc7thk4zfwshg4

Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration [article]

Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara, Ginger Tsueng, Andrew I Su, Chunlei Wu
2017 bioRxiv   pre-print
Here, we have implemented JSON for Linking Data (JSON-LD) technology on the BioThings APIs that we have developed, MyGene.info, MyVariant.info and MyChem.info.  ...  While usage of a common data format offers significant advantages, that alone is not sufficient for rich integrative queries across APIs.  ...  The information for data, workflows and scripts used in the paper is available under an Apache software license at https://github.com/biothings/JSONLD_BioThings_API_DEMO .  ... 
doi:10.1101/167353 fatcat:e632pc7zzrfk3m72et427ghjla

Sublethal effects of imidacloprid on targeting muscle and ribosomal protein related genes in the honey bee Apis mellifera L

Yan-Yan Wu, Qi-Hua Luo, Chun-Sheng Hou, Qiang Wang, Ping-Li Dai, Jing Gao, Yong-Jun Liu, Qing-Yun Diao
2017 Scientific Reports  
We treated Apis mellifera L. with sublethal concentrations of imidacloprid (0.1, 1 and 10 ppb) and determined the effect on behaviors and the transcriptomic changes.  ...  Considering the ribosomal and extra-ribosomal functions of the ribosomal proteins, we hypothesized that imidacloprid also causes cell dysfunction.  ...  This work was supported by the National Natural Science Foundation of China (31402148), the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2016-IAR) and Chinese Central Public-interest  ... 
doi:10.1038/s41598-017-16245-0 pmid:29162882 pmcid:PMC5698328 fatcat:qxupufj7hzg5dmlrjzdkbepjia
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