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diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index 296bef6..ade902d 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -3,7 +3,6 @@ # C-c C-e h h publish # C-c ! insert date (use . for active agenda, C-u C-c ! for date, C-u C-c . for time) # C-c C-t task rotate -# RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png #+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" /> @@ -14,8 +13,12 @@ * Table of Contents :TOC:noexport: - [[#uploading-data][Uploading Data]] - [[#introduction][Introduction]] - - [[#step-1-sequence][Step 1: Sequence]] - - [[#step-2-metadata][Step 2: Metadata]] + - [[#step-1-upload-sequence][Step 1: Upload sequence]] + - [[#step-2-add-metadata][Step 2: Add metadata]] + - [[#obligatory-fields][Obligatory fields]] + - [[#optional-fields][Optional fields]] + - [[#step-3-submit-to-covid-19-pubseq][Step 3: Submit to COVID-19 PubSeq]] + - [[#trouble-shooting][Trouble shooting]] * Introduction @@ -23,14 +26,120 @@ The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a public resource for global comparisons. Compute it triggered on upload. Read the [[./about][ABOUT]] page for more information. -* Step 1: Sequence +* Step 1: Upload sequence + +To upload a sequence in the [[http://covid19.genenetwork.org/][web upload page]] hit the browse button and +select the FASTA file on your local hard disk. We start with an assembled or mapped sequence in FASTA format. The PubSeq uploader contains a [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/qc_fasta.py][QC step]] which checks whether it is a likely SARS-CoV-2 sequence. While PubSeq deduplicates sequences and never -overwrites metadata it probably pays to check whether your data +overwrites metadata, you may still want to check whether your data already is in the system by querying some metadata as described in -[[./blog?id=using-covid-19-pubseq-part1][Query metadata with SPARQL]]. +[[./blog?id=using-covid-19-pubseq-part1][Query metadata with SPARQL]] or by simply downloading and checking one +of the files on the [[./download][download]] page. We find GenBank [[https://www.ncbi.nlm.nih.gov/nuccore/MT536190][MT536190.1]] has not +been included yet. A FASTA text file can be [[https://www.ncbi.nlm.nih.gov/nuccore/MT536190.1?report=fasta&log$=seqview&format=text][downloaded]] to your local +disk and uploaded through our [[./][web upload page]]. Make sure the file does +not include any HTML! + +Note: we currently only allow FASTA uploads. In the near future we'll +allow for uploading raw sequence files. This is important for creating +an improved pangenome. + +* Step 2: Add metadata + +The [[./][web upload page]] contains fields for adding metadata. Metadata is +not only important for attribution, is also important for +analysis. The metadata is available for queries, see [[./blog?id=using-covid-19-pubseq-part1][Query metadata +with SPARQL]], and can be used to annotate variations of the virus in +different ways. + +A number of fields are obligatory: sample id, date, location, +technology and authors. The others are optional, but it is valuable to +enter them when information is available. Metadata is defined in this +[[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml][schema]]. From this schema we generate the input form. Note that +opitional fields have a question mark in the ~type~. You can add +metadata yourself, btw, because this is a public resource! See also +[[./blog?id=using-covid-19-pubseq-part5][Modify metadata]] for more information. + +To get more information about a field click on the question mark on +the web form. Here we add some extra information. + +** Obligatory fields + +*** Sample ID (sample_id) + +This is a string field that defines a unique sample identifier by the +submitter. In addition to sample_id we also have host_id, +provider_sample_id and submitter_sample_id where host is the host the +sample came from, provider sample is the institution sample id and +submitter is the submitting individual id. host_id is important when +multiple sequences come from the same host. Make sure not to have +spaces in the sample_id. + +Here we add the GenBank ID MT536190.1. + +*** Collection date + +Estimated collection date. The GenBank page says April 6, 2020. + +*** Collection location + +A search on wikidata says Los Angelos is +https://www.wikidata.org/entity/Q65 + +*** Sequencing technology + +GenBank entry says Illumina, so we can fill that in + +*** Authors + +GenBank entry says 'Lamers,S., Nolan,D.J., Rose,R., Cross,S., Moraga +Amador,D., Yang,T., Caruso,L., Navia,W., Von Borstel,L., Hui Zhou,X., +Freehan,A. and Garcia-Diaz,J.', so we can fill that in. + +** Optional fields + +All other fields are optional. But let's see what we can add. + +*** Host information + +Sadly, not much is known about the host from GenBank. A little +sleuthing renders an interesting paper by some of the authors titled +[[https://www.medrxiv.org/content/10.1101/2020.04.24.20078691v1][SARS-CoV-2 is consistent across multiple samples and methodologies]] +which dates after the sample, but has no reference other than that the +raw data came from the SRA database, so it probably does not describe +this particular sample. We don't know what this strain of SARS-Cov-2 +did to the person and what the person was like (say age group). + +*** Collecting institution + +We can fill that in. + +*** Specimen source + +We have that: nasopharyngeal swab + +*** Source database accession + +Genbank which is http://identifiers.org/insdc/MT536190.1#sequence. +Note we plug in our own identifier MT536190.1. + +*** Strain name + +SARS-CoV-2/human/USA/LA-BIE-070/2020 + +* Step 3: Submit to COVID-19 PubSeq + +Once you have the sequence and the metadata together, hit +the 'Add to Pangenome' button. The data will be checked, +submitted and the workflows should kick in! +** Trouble shooting -* Step 2: Metadata +We got an error saying: {"stem": "http://www.wikidata.org/entity/",... +which means that our location field was not formed correctly! After +fixing it to look like http://www.wikidata.org/entity/Q65 (note http +instead on https and entity instead of wiki) the submission went +through. Reload the page (it won't empty the fields) to re-enable the +submit button. |