Provide a curated list of quality BCOs for example

[HadleyKing]

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

• Exemplar BCOs referenced in publications
• BCOs that have important features for testing to be included in the example DB

@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]

• BCOs that have been referenced in a publication
• duf1220 domain of unknown function, copy number variation
• cwl: https://github.com/biocompute-objects/bcotool/blob/main/data_tests/collapsed-cwl-blastn-homologs.json
• gdc pipeline
• neoantigen pipeline**

[kee007ney]

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]

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

[tiwa1154]

Outcome: default search shows curated list of BCOs

[tiwa1154]

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]

@tiwa1154

can you add these two bcos to that list:

• https://biocomputeobject.org/BCO_022530/2.2
• https://biocomputeobject.org/BCO_022531/2.2

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

[kee007ney]

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