Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Readme updates #430

Merged
merged 3 commits into from
Feb 21, 2024
Merged

Readme updates #430

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
21b8103
Update README.md
HadleyKing Feb 13, 2024
bd42cb1
Test Commit
cwoodside1278 Feb 13, 2024
4304768
Taking the source code excerpt from README and
cwoodside1278 Feb 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
39 changes: 35 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,16 @@
# data.argosdb
# FDA-ARGOS: ARGOSDB

Repository for data files and schema definitions for ARGOS rpoject.
Repository for data files and schema definitions for ARGOS project.
For additional details on project information and assembly QC see:

* [ARGOSDB](https://data.argosdb.org/)
* [NCBI Bioproject](https://www.ncbi.nlm.nih.gov/bioproject/231221)
* [Project Information](https://www.fda.gov/emergency-preparedness-and-response/mcm-regulatory-science/expanding-next-generation-sequencing-tools-support-pandemic-preparedness-and-response)

## Introduction
FDA-ARGOS database updates may help researchers rapidly validate diagnostic tests and use qualified genetic sequences to support future product development

As of September 2021, Embleema and George Washington University have been conducting bioinformatic research and system development, focusing on expanding the FDA-ARGOS database. This project expands datasets publicly available in FDA-ARGOS, improves quality control by developing quality matrix tools and scoring approaches that will allow the mining of public sequence databases, and identifies high-quality sequences for upload to the FDA-ARGOS database as regulatory-grade sequences. Building on expansions during the COVID-19 pandemic, this project aims to further improve the utility of the FDA-ARGOS database as a key tool for medical countermeasure development and validation.

## Data_files
Space for raw or processed data files
Expand All @@ -9,7 +19,22 @@ _
space for documentation

## Schema
Houses the ARGOS data schemas by release version
Houses the ARGOS data schemas by release version:

Current: [v1.5](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v1.5)
[v1.4](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v1.4)
[v1.3](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v1.3)
[v1.2](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v1.2)
[v1.1](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v1.1)
[v1.0](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v1.0)
[v0.9](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v0.9)
[v0.8](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v0.8)
[v0.7](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v0.7)
[v0.6](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v0.6)
[v0.5](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v0.5)
[v0.4](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v0.4)
[v0.3](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v0.3)
[v0.1](https://github.com/FDA-ARGOS/data.argosdb/tree/main/schema/v0.1)

## lib
For scripts and sutch
Expand Down Expand Up @@ -39,4 +64,10 @@ For Example:
```
> python lib/dictionary_utils.py validate -i https://raw.githubusercontent.com/FDA-ARGOS/data.argosdb/v0.5/data_files/test_SRA_ngsQC.tsv -s https://raw.githubusercontent.com/FDA-ARGOS/data.argosdb/v0.5/schema/v0.5/non-core/SRA_ngsQC.json
```
should give you the same results.
should give you the same results.


## Citations
Sichtig, H., Minogue, T., Yan, Y. et al. FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nat Commun 10, 3313 (2019). https://doi.org/10.1038/s41467-019-11306-6


31 changes: 31 additions & 0 deletions lib/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,3 +20,34 @@ Optional parameters:
Example usage:

`./biosample_complete.sh -f biosample_ids.txt -n ngsQC_HIVE.tsv -b ARGOS_000028 -s v1.12`

## lib
For scripts and sutch


### Validating a data file against a schema:
Assume you wanted to validate a flie of the type`SRA_ngsQC`(this same process should work for any of the types we have defined).

- The data file is `/data_files/test_SRA_ngsQC.tsv`
- The schema for a `SRA_ngsQC` data file is `/schema/v0.5/non-core/SRA_ngsQC.json`

For illitstration purposes cell `T6` in our example data file has been modified. The schema says that the value has to be less than 1, as `gc_ content` is a percentage. The example data sheet has a value of `10.63682374` in that cell, and the following error shoudl be thrown:

`Line 5 failed. '10.63682374' does not match '^[+-]?([0]+\\.?[0-9]*|\\.[0-9]+)$`

From the project root run:

```shell
> python lib/dictionary_utils.py validate -i data_files/test_SRA_ngsQC.tsv -s schema/v0.5/non-core/SRA_ngsQC.json
```

### Validating a data file against a schema with remote files:

Both the schema [`-s`] and input file [`-i`] values can take a URL, assuming they are formatted correctly and resolvable.

For Example:
```
> python lib/dictionary_utils.py validate -i https://raw.githubusercontent.com/FDA-ARGOS/data.argosdb/v0.5/data_files/test_SRA_ngsQC.tsv -s https://raw.githubusercontent.com/FDA-ARGOS/data.argosdb/v0.5/schema/v0.5/non-core/SRA_ngsQC.json
```
should give you the same results.