Format Development

Sample and sequencing meta data fields

The meta fields for the sample and sequencing are based on NCBI naming schemes especially from SRA submission portal for human-associated pathogen. These are similar to the MiXS standards set by the Genomics Standards Consortium (GSC)

Sample

SRA for sample meta: https://submit.ncbi.nlm.nih.gov/biosample/template/?package-0=MIGS.eu.human-associated.6.0&action=definition
GSC for MIGS eukaryote: https://genomicsstandardsconsortium.github.io/mixs/0010002/

Example file for SRA submission

MIGS.eu.human-associated.6.0.xlsx

Sequencing

SRA sequencing meta: https://www.ncbi.nlm.nih.gov/sra/docs/submitportal/#6-sra-metadata
GSC for MIGS eukaryote: https://genomicsstandardsconsortium.github.io/mixs/0010002/

Example file for SRA submission

SRA_metadata.xlsx

Python implementation

Linkml generates a datamodel file with all classes: https://github.com/PlasmoGenEpi/portable-micorhaplotype-object/blob/main/src/plasmo_tar_amp_schema/datamodel/plasmo_tar_amp_schema.py

Tools

Started development of a tool called pmotools. Python implementation can be found here: https://github.com/PlasmoGenEpi/pmotools-python/tree/develop

From GEM meeting

adding header with info on each field
adding version to header
random access ability

---
title: Format Development 
---

<script src="https://code.jquery.com/jquery-2.2.2.min.js"></script>

<script>
$(document).ready(function() {
    document.querySelectorAll('.downloadLink').forEach(function(e) { e.setAttribute('download', e.text); });
    document.querySelectorAll('.downloadLink').forEach(function(e) { e.innerHTML = '<i class="fa fa-download"></i>  ' + e.text; });
});
</script>

```{r setup, echo=FALSE}
source("../common.R")
```

# Sample and sequencing meta data fields 

The meta fields for the sample and sequencing are based on NCBI naming schemes especially from SRA submission portal for human-associated pathogen. These are similar to the [MiXS standards](https://genomicsstandardsconsortium.github.io/mixs/) set by the [Genomics Standards Consortium (GSC)](https://www.gensc.org/)

## Sample 

SRA for sample meta: <https://submit.ncbi.nlm.nih.gov/biosample/template/?package-0=MIGS.eu.human-associated.6.0&action=definition>  
GSC for MIGS eukaryote: <https://genomicsstandardsconsortium.github.io/mixs/0010002/>   

Example file for SRA submission   
```{r}
#| results: asis
#| echo: false

cat(createDownloadLink("MIGS.eu.human-associated.6.0.xlsx"))
```

## Sequencing  

SRA sequencing meta: <https://www.ncbi.nlm.nih.gov/sra/docs/submitportal/#6-sra-metadata>  
GSC for MIGS eukaryote: <https://genomicsstandardsconsortium.github.io/mixs/0010002/>   

Example file for SRA submission 
```{r}
#| results: asis
#| echo: false

cat(createDownloadLink("SRA_metadata.xlsx"))
```


# Python implementation 

Linkml generates a datamodel file with all classes: <https://github.com/PlasmoGenEpi/portable-micorhaplotype-object/blob/main/src/plasmo_tar_amp_schema/datamodel/plasmo_tar_amp_schema.py>


# Tools  

Started development of a tool called pmotools. Python implementation can be found here: <https://github.com/PlasmoGenEpi/pmotools-python/tree/develop>




# From GEM meeting

- [ ] adding header with info on each field 
- [ ] adding version to header   
- [ ] random access ability  



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