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Prompted by a lot of the recent work of adding new pathogens (e.g. [seasonal-cov](https://github.com/nextstrain/nextstrain.org/pull/939) and [rabies](https://github.com/nextstrain/nextstrain.org/pull/…
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Both IDO and OBI have term 'pathogen role'. However, the term was defined slightly different.
[OBI: pathogen role](http://purl.obolibrary.org/obo/OBI_0000718): Pathogen role is a role which inheres i…
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- [ ] 1. Allow users to download all segments (now we make them choose:
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- [ ] 2. Maybe don't show empty sequences of in sequence viewer:
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It would be good to have a standard list of pathogens we look for in the workflow, with a standard way of presenting the results. We can use the [select agent list](https://selectagents.gov/sat/list.h…
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https://github.com/nextstrain/conda-base/blob/02cf82eee26e39b6772c2cdb47b7cca622bd3df0/.github/workflows/ci.yaml#L138
Expanding the above TODO into a GitHub issue.
Currently, pathogen CI only ru…
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### Context
Prompted by https://github.com/nextstrain/yellow-fever/pull/7#issuecomment-2223488890 and https://github.com/nextstrain/rabies/pull/2#issuecomment-2229140713.
### Description
We …
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There are existing resources that we can point to as starting point:
- [Alli's Epi Handbook](https://alliblk.github.io/genepi-book/)
- [Nextstrain VEME tutorial](https://github.com/blab/veme-2022) …
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ISARIC Core CRF captures serology or genomic results indicating the type of pathogen. For example Influenza A/H3N2, Dengue DENV1, Hepatitis type B. WHO T0 form indicates collection of pathogenic agent…
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### Model
ESKAPE pathogen inhibition - eos5xng
### Molecules
O=C(C(C)C)C1=C(O)C=C(OC)C=C1/C=C/C2=CC=C(O)C=C2
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Hi Anni,
First many thanks for your contribution in AMR risk assessment. It's very useful.
Here I have two questions. The first one is about Rank-IV ARGs. From our metagenomics analysis we found tha…