Biology subjects

Lelong, S.

Publications and source records attributed to Lelong, S..

4 recordsLinked to original sources

bioRxiv2021

BioThings SDK: a toolkit for building high-performance data APIs in biomedical research

SummaryTo meet the increased need of making biomedical resources more accessible and reusable, Web APIs or web services have become a common way to disseminate knowledge sources. The BioThings APIs are a collection of high-performance, scalable, annotation as a service APIs that automate the integration of biological annotations from disparate data sources. This collection of APIs currently includes MyGene.info, MyVariant.info, and MyChem.info for integrating annotations on genes, variants, and chemical compounds, respectively. These APIs are used by both individual researchers and application developers to simplify the process of annotation retrieval and identifier mapping. Here, we describe the BioThings Software Development Kit (SDK), a generalizable and reusable toolkit for integrating data from multiple disparate data sources and creating high-performance APIs. This toolkit allows users to easily create their own BioThings APIs for any data type of interest to them, as well as keep APIs up-to-date with their underlying data sources. Availability and implementationThe BioThings SDK is built in Python and released via PyPI (https://pypi.org/project/biothings/). Its source code is hosted at its github repository (https://github.com/biothings/biothings.api).

bioinformatics↗

bioRxiv2019

Retrieval of whole human genome clinical variant information through search motors

The interpretation of variation in the human genome constitutes one of the most pressing challenges in biomedicine. There are many academic and proprietary resources that provide annotation, interpretation, scoring and knowledge of genetic variants under multiple access modalities. For these resources, information is available through portals, wikis, APIs, curated content and databases, and pipelines. Here we explore the use of search motors to provide facilitated access to the main sources of information that are used by clinical geneticists and researchers. We also support the browsing experience with natural language processing and automated summaries of available information. The resulting tool, ai-OMNI.com, is intrinsically flexible, expandable and intuitive, thus providing a different experience for querying the human genome for the consequences of variation.

genomics↗

bioRxiv2017

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

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.\n\nResultsHere, 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.\n\nConclusionsWe believe that this pattern offers a generalizable solution for interoperability of APIs in the life sciences.

bioinformatics↗

bioRxiv2017

WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata.

With the advancement of genome sequencing technologies, new genomes are being sequenced daily. While these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources dont exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomic data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.

genomics↗