ArticleBMC bioinformatics2018
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology.Bioinformatics (Oxford, England) · 2024Article
- MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes.Nucleic acids research · 2023Article
- ARAX: a graph-based modular reasoning tool for translational biomedicine.Bioinformatics (Oxford, England) · 2023Article
- The Exposome and Nutritional Pharmacology and Toxicology: A New Application for Metabolomics.Exposome · 2023Article
- KGML-xDTD: a knowledge graph-based machine learning framework for drug treatment prediction and mechanism description.GigaScience · 2022Article
- RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine.BMC bioinformatics · 2022Article
- Pathway information extracted from 25 years of pathway figures.Genome biology · 2020Article
- MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons.Scientific reports · 2020Article
- Article
- BrAPI-an application programming interface for plant breeding applications.Bioinformatics (Oxford, England) · 2019Article
- Mining data and metadata from the gene expression omnibus.Biophysical reviews · 2019Review
- An effective biomedical data migration tool from resource description framework to JSON.Database : the journal of biological databases and curation · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
backgroundApplication Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different research teams have adopted Javascript Object Notation (JSON) as their primary data format. While usage of a common data format offers significant advantages, that alone is not sufficient for rich integrative queries across APIs.
resultsHere, 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 . JSON-LD provides a standard way to add semantic context to the existing JSON data structure, for the purpose of enhancing the interoperability between APIs. We demonstrated several use cases that were facilitated by semantic annotations using JSON-LD, including simpler and more precise query capabilities as well as API cross-linking.
conclusionsWe believe that this pattern offers a generalizable solution for interoperability of APIs in the life sciences.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.