Populate Glossary Wiki: Harmonize terminology across the whole project

[almosnow]

• Contig - One of the (many) assembled contigs from a Run
• Read - Synonym of run
• Run - Technically, sequence data as it came out from one sequencing "run". Colloquially, one entry in SRA (?)
• Sample - One sample entry in the BioSample DB
• ...

[almosnow]

Should this be a wiki entry instead?

[ababaian]

A Glossary wiki page is a good idea. Populate it as neccesary.

[ababaian]

By the end of Sprint 3 (Oct 21), each developer should add at least 5 meaningful project-specific terms to the Open Virome Glossary

See: https://github.com/serratus-bio/open-virome/wiki/Glossary

• [ ] Artem
• [ ] Alex
• [ ] Luke
• [ ] Forbes

[ababaian]

I updated the bioSample term:

• bioSample: A distinct "biological sample" entity as defined in the bioSample Metadata database. bioSamples are assigned membership to one or more parent bioProject. Each bioSample can have one or more sequences (GenBank) or runs (Sequence Read Archive) associated with it. See: bioSample Database

[ababaian]

Minor correction in Library

From:

• Library: A sequencing library, usually alludes to one particular vial(?) coming from a biological sample that has been prepared for sequencing. Avoid using library to refer to an experiment or a run; use the more appropriate term instead.

To:

• Library: Synonym for Run. Used to describe a specific "Sequencing Library", or dataset.

[ababaian]

• [ ] Everyone: document which definitions you completed
• [ ] Everyone: Review/revise all terms; divided equally amongst everyone.

Missing Terms - Ecology

• STAT, with link to paper
• Alpha Diversity / Beta Diversity
• Geocoding
• Biome

Missing Terms - Virology

• Segmented / Bipartite

Missing Terms - Graph

• Graph / Network
• make Monopartite vs. Bipartite Network
• make Homogenous vs. Heterogenous Network