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Fix typos, update links
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bussec committed Feb 22, 2018
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15 changes: 3 additions & 12 deletions NCBI_implementation/README.md
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Expand Up @@ -30,7 +30,7 @@ Submission of AIRR sequencing data and metadata to NCBI's public data repositori
4. Generate a DOI for the protocol describing how raw sequencing data were processed using [Zenodo](https://zenodo.org) or an equivalent DOI-granting service.
5. Submit processed sequencing data with sequence-level annotations to [GenBank](https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/) using AIRR feature tags.

For step-by-step instructions on carrying out theses steps an AIRR study submission, see [here](https://www.overleaf.com/read/tytddwptgkhb).
For step-by-step instructions on carrying out theses steps an AIRR study submission, see [here](http://docs.airr-community.org/en/latest/miairr/overview.html).


### How to cite?
Expand All @@ -47,15 +47,6 @@ commented out until the actual MiAIRR publication it out and can be referenced t
-->


### Report an issue to help us improving MiAIRR
### Further information

https://waffle.io/airr-community/airr-standards


### Contact

For further information about the MiAIRR standard please contact
[Syed **Ahmad** Chan Bukhari](mailto:[email protected]?subject=MiAIRR%20Standard) or
[Steven Kleinstein](mailto:[email protected]?subject=MiAIRR%20Standard).

***
For further information on this and other AIRR Community Data Standards see [here](https://github.com/airr-community/airr-standards).
6 changes: 3 additions & 3 deletions docs/miairr/manual_miairr_ncbi.rst
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Expand Up @@ -127,11 +127,11 @@ MiAIRR data submission to GenBank/TLS

Processed sequence data will be submitted to the "Targeted Locus Study"
(TLS) section of GenBank. The details of this submission process are
currently still finalized. Basically the procedure is identical to a
conventional GenBank submission with the exception of additional
currently still being finalized. Basically the procedure is identical to
a conventional GenBank submission with the exception of additional
keywords marking it as TLS submission.

Non-functional records should be removed before the data submission or
Non-productive records should be removed before the data submission or
use an alternative annotation as described in the specification
document.

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8 changes: 4 additions & 4 deletions docs/miairr/specification_miairr_ncbi.rst
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Expand Up @@ -217,10 +217,10 @@ The header MUST contain all of the following elements:
information on data processing (MiAIRR data set 5) as ``REMARK``
within a ``REFERENCE`` [4]_ (ENA: ``RX`` line).

- OPTIONAL: The use of `structured records`_ is currently evalutated
- OPTIONAL: The use of `structured comments`_ is currently evalutated
for use in future versions of the MiAIRR standard.

.. _`structured records`: https://www.ncbi.nlm.nih.gov/genbank/structuredcomment/
.. _`structured comments`: https://www.ncbi.nlm.nih.gov/genbank/structuredcomment/


Feature table
Expand Down Expand Up @@ -264,8 +264,8 @@ SHOULD contain the following keys/qualifiers:
Note that additional qualifiers might be REQUIRED by GenBank to
harmonize the GenBank record with the BioSample referenced by it in the
header. A list of known BioSample keyword and GenBank qualifiers that
MUST contain the same information can be found below. Whether (and if
yes in which direction) the existence of a keyword/qualifiers triggers
MUST contain the same information can be found below. Whether (and in
which direction) the existence of a keyword/qualifiers triggers
a requirement in the corresponding record is currently unknown. Please
report any undocumented requirements surfacing during submission to the
MiAIRR team.
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