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add cohort-subs-guide.rst updates to pathogen-subs-guide.rst -updates new link to pathogen portal -improves wording and fixes typos
fixes link to bash script example
faq/cohort-subs-guide.rst
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| 2. Create the child Samples in additional database resources | ||
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| The next step is to create your datasets in the correct database for the data type. The `EBI submissions wizard | ||
| <https://www.ebi.ac.uk/submission/>`_ can help direct you to a resource to deposit your data. | ||
| We can reccommend the following database resources for common data types: | ||
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| - For sensitive human nucleotide records and human clinical epidemiological data which requires controlled access, please | ||
| contact the `EGA (European Genome Phenome Archive) <https://ega-archive.org/>`_ to start a submission. | ||
| - For expression data, or uncategorsied datasets, please use `ArrayExpress/BioStudies <https://www.ebi.ac.uk/biostudies/arrayexpress>`_ | ||
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| After the datasets have been submitted in the appropriate databases, the required child Samples for linking can be created. | ||
| The child samples will represent their relationship to the top-level Sample. Different samples can be used for different | ||
| data types **and** for different time points. Please contact us if you have any doubts about setting up your sample structure. | ||
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I would split this out into 2 sections for clarity - e.g.:
2. Submit other data types to appropriate database resources
3. Create the child samples for linking
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step 2 is now split into steps 3 and 4
faq/cohort-subs-guide.rst
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| For example, in the first linked dataset, the `EMC study <https://www.ebi.ac.uk/about/news/updates-from-data-resources/pathogens-portal-linked-dataset/>`_, | ||
| the BioSamples relationship is as follows: |
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I think it would also be helpful to include a link here to the IDTK page, as it contains more diagrams: https://www.infectious-diseases-toolkit.org/showcase/linked-cohort-data
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IDTK added with link title '[Erasmus Medical Cemter (EMC) study'
faq/cohort-subs-guide.rst
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| There is also a `python script<https://www.ebi.ac.uk/biosamples/docs/references/api/submit#_submit_curation_object>`_ | ||
| which can be used to create the sample relationships. Please contact ena-path-collabs@ebi.ac.uk for technical support |
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I see you have not linked the python script here, but I was wondering if we can hold off on sharing that just yet anyway - as it's only really been tested on one use-case.
We have another 2 linking use-cases coming up that I am actively working on, so would like to test the script on at least one of those before sharing
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this section has been removed
z-w123
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z-w123
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Hi Jasmine, I have added a few comments, if you could please take a look that would be great
- add sample structure image - updates to doc structure
fix Biosamples curation link
2 participants
-fixes links and updates pathgoens submissions guide