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biocompute-objects / bco_api

The master repository for the JSON API.
MIT License
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Provide a curated list of quality BCOs for example #312

Closed HadleyKing closed 4 months ago

HadleyKing commented 7 months ago

We need a list of BCOs that can fulfill two main functions:

@tiwa1154 I want to use the table below to track this issue

BCO ID BCO Name Reason for picking URL In Publication Publication URL is working
1. https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000038/1.0 R Safety Assessment Algorithm for Aluminum in Infant Vaccines Algorithm developed by CBER and has associated publication NA Yes
2. https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 WGS Simulation of DUF1220 Regions Seems to be a more complete BCO with good provenance and usability domain, and execution and error domain. NA Yes
3. Figshare RNA-Seq Differential Expression & Pathway Analysis Referenced in https://f1000research.com/articles/9-1144/v1 No
4. https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_069535/1.0 Merck RVDB (v18) Curation Pipeline Referenced in https://www.sciencedirect.com/science/article/pii/S1359644624000096?via%3Dihub#s0060. v2.0 is also available
5. https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_031929/1.0 In-silico viral reads generation from Human Adenovirus, West Nile virus, Hepatitis B virus, and Lassa virus sequences. Referenced in https://www.sciencedirect.com/science/article/pii/S1359644624000096?via%3Dihub#s0060.
6. Couldn't find in BCODB, S3 file Viral metagenomic analysis using the lenient alignment settings Referenced in https://www.sciencedirect.com/science/article/pii/S1359644624000096?via%3Dihub#s0060.
7. Couldn't find in BCODB, S4 file Viral metagenomics analysis using the stringent alignment settings Referenced in https://www.sciencedirect.com/science/article/pii/S1359644624000096?via%3Dihub#s0060. Some BCOs were mentioned in this article Table 2 but not exist in BCODB
8. https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000062/1.0 HCV1a ledipasvir resistance SNP detectio Referenced in https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000099#sec013
ChinweokeO commented 5 months ago
kee007ney commented 5 months ago

Teaching example with strong biological back story, error domain, advanced i/o features (DUF1220): https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000277/4.0

Published Merck pipeline for creating a database: https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_069535/2.0

kee007ney commented 5 months ago

CWL example (not yet published in the Portal): https://biocomputeobject.org/builder?https%3A%2F%2Fbiocomputeobject.org%2FDNAN_000009%2FDRAFT=

tiwa1154 commented 5 months ago

Outcome: default search shows curated list of BCOs

tiwa1154 commented 4 months ago

I have created a SP for the list of BCOs: https://gwu0.sharepoint.com/sites/BioCompute-GRP/_layouts/15/doc.aspx?sourcedoc={09f5ed86-3813-4f7e-af25-9a6244bcaefa}&action=edit

HadleyKing commented 4 months ago

@tiwa1154

can you add these two bcos to that list:

Also I am not sure we should include https://biocomputeobject.org/BCO_000062/1.0.

kee007ney commented 4 months ago

Please add this BCO to the list, then we can close the ticket. https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_095545/1.2 @HadleyKing