The EMBL-EBI search and sequence analysis tools APIs in 2019
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Summary
The latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability are described.
- Type
- article
- Published
- 2019-04-12
- Cited by
- 3,792
- References
- 35
- Access
- Open access
- OpenAlex
- https://openalex.org/W2938574745
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:109941489
Keywords
Discoverability, Interoperability, World Wide Web, Computer science, Information retrieval
References
- Europe PMC: a full-text literature database for the life sciences and platform for innovation
- NCBI’s Database of Genotypes and Phenotypes: dbGaP
- EMBOSS: the European Molecular Biology Open Software Suite.
- PomBase 2015: updates to the fission yeast database
- Improved tools for biological sequence comparison.
- Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs.
- Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood
- InterProScan 5: genome-scale protein function classification
- The IPD and IMGT/HLA database: allele variant databases
- Jalview Version 2—a multiple sequence alignment editor and analysis workbench
- Updates to BioSamples database at European Bioinformatics Institute
- ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins
- The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates
- BLAST+: architecture and applications
- Tools and data services registry: a community effort to document bioinformatics resources
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- The European Bioinformatics Institute in 2016: Data growth and integration
- A new Ontology Lookup Service at EMBL-EBI
- Common Workflow Language, v1.0
- The ChEMBL database in 2017
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- The gene expression and bioinformatic analysis of choline trimethylamine-lyase (CutC) and its activating enzyme (CutD) for gut microbes and comparison with their TMA production levels
- Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services
- Deep Functional Profiling Facilitates the Evaluation of the Antibacterial Potential of the Antibiotic Amicoumacin
- Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility
- The SINEB1 element in the long non-coding RNA Malat1 is necessary for TDP-43 proteostasis
- The C-Terminal Domains SnRK2 Box and ABA Box Have a Role in Sugarcane SnRK2s Auto-Activation and Activity
- Caldicellulosiruptor bescii regulates pilus expression in response to the polysaccharide, xylan
- DNAJC proteins and pathways to parkinsonism
- AimB is a small protein regulator of cell size and MreB assembly
- A review of alignment based similarity measures for web usage mining
- Of capsid structure and stability: the partnership between charged residues of E-loop and P-domain of the bacteriophage P22 coat protein
- Aequorea victoria’s secrets
- Transcriptome analysis reveals the importance of the immune system during early pregnancy in sheep
- Investigation of molecular interactions of prenylflavonoids at GABAA receptor subtypes
- Delineation of the olive pollen proteome and its allergenome unmasks cyclophilin as a relevant cross-reactive allergen.
- Integrated transcriptomic and functional immunological approach for assessing the invasiveness of bivalve alien species
- Polymorphism analyses and protein modelling inform on functional specialization of Piwi clade genes in the arboviral vector Aedes albopictus
- Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the Gram-positive model organism Streptococcus mutans
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