diff --git a/NCBI_implementation/README.md b/NCBI_implementation/README.md index 2d741a67f..ca5e49fb3 100644 --- a/NCBI_implementation/README.md +++ b/NCBI_implementation/README.md @@ -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? @@ -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:ahmad.chan@yale.edu?subject=MiAIRR%20Standard) or -[Steven Kleinstein](mailto:steven.kleinstein@yale.edu?subject=MiAIRR%20Standard). - -*** +For further information on this and other AIRR Community Data Standards see [here](https://github.com/airr-community/airr-standards). diff --git a/docs/miairr/manual_miairr_ncbi.rst b/docs/miairr/manual_miairr_ncbi.rst index 476da4e2e..a13c1cc21 100644 --- a/docs/miairr/manual_miairr_ncbi.rst +++ b/docs/miairr/manual_miairr_ncbi.rst @@ -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. diff --git a/docs/miairr/specification_miairr_ncbi.rst b/docs/miairr/specification_miairr_ncbi.rst index d3f4c1828..f196b09bc 100644 --- a/docs/miairr/specification_miairr_ncbi.rst +++ b/docs/miairr/specification_miairr_ncbi.rst @@ -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 @@ -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.