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diff --git a/doc/web/about.org b/doc/web/about.org index 29a80bf..d8d7f73 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -3,6 +3,7 @@ * Table of Contents :TOC:noexport: - [[#what-is-the-public-sequence-resource-about][What is the 'public sequence resource' about?]] + - [[#presentations][Presentations]] - [[#who-created-the-public-sequence-resource][Who created the public sequence resource?]] - [[#how-does-the-public-sequence-resource-compare-to-other-data-resources][How does the public sequence resource compare to other data resources?]] - [[#why-should-i-upload-my-data-here][Why should I upload my data here?]] @@ -17,21 +18,54 @@ - [[#how-do-i-change-the-work-flows][How do I change the work flows?]] - [[#how-do-i-change-the-source-code][How do I change the source code?]] - [[#should-i-choose-cc-by-or-cc0][Should I choose CC-BY or CC0?]] - - [[#are-there-also-variant-in-the-RDF-databases]][Are there also variant in the RDF databases?] + - [[#are-there-also-variant-in-the-rdf-databases][Are there also variant in the RDF databases?]] - [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]] - - [[#do-you-have-any-checks-or-concerns-if-human-sequence-accidentally-submitted-to-your-service-as-part-of-a-fastq][Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq?] - - [[#does-PubSeq-support-only-SARS-CoV-2=data]][Does PubSeq support only SARS-CoV-2 data?] + - [[#do-you-have-any-checks-or-concerns-if-human-sequence-accidentally-submitted-to-your-service-as-part-of-a-fastq-][Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *]] + - [[#does-pubseq-support-only-sars-cov-2-data][Does PubSeq support only SARS-CoV-2 data?]] - [[#how-do-i-communicate-with-you][How do I communicate with you?]] + - [[#citing-pubseq][Citing PubSeq]] - [[#who-are-the-sponsors][Who are the sponsors?]] * What is the 'public sequence resource' about? -The *public sequence resource* aims to provide a generic and useful -resource for COVID-19 research. The focus is on providing the best -possible sequence data with associated metadata that can be used for -sequence comparison and protein prediction. - -We were at the *Bioinformatics Community Conference 2020*! Have a look at the [[https://bcc2020.sched.com/event/coLw]][video talk] ([[https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing]][alternative link]) and the [[https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing]][poster]. +PubSeq, the *public sequence resource*, aims to provide a generic and +useful resource for COVID-19 research. The focus is on providing the +best possible sequence data with associated metadata that can be used +for sequence comparison and protein prediction. + +Just to avoid the notion that PubSeq is a biorepository: it is far +more than that. We are not competing with the likes of GenBank, +EBI/ENA and GISAID - in fact, PubSeq sources much of the data from +those and they get ours. + +There is no conflict of posting data to multiple repositories. + +It is better to view PubSeq as an *open precision medicine initiative* that +allows for early detection of new variants and strains; very valuable +for both testing and treatment. We have live analysis work flows that +run on uploading a new sequence. Contributing sequences helps the +overall detection. At this moment the output is limited. We will soon +add interactive discovery tools. Uploading data from a sequencer will +give researchers all information they want in 5 hours *without any +bioinformatics knowledge*. We may even provide workflows that take +data straight from the sequencer. In fact, you get very little out of +existing biorepositories, in our opinion, unless you have solid +bioinformatics support. And even then there is the question about +comparing data that was created using different technologies and +workflows. How do you deal with that? + +With PubSeq we are in a position to reanalyse that data from raw +material when new insights arise. It is likely that COVID19 will be +around for another year at least. After that we should prepare for +the next pandemic. PubSeq is meant for that. We take the long view and +it will only get more powerful. Who knows: maybe the live analysis +part of PubSeq will be an approach that other biorepositories will +follow. + +* Presentations + +We presented at the BOSC 2020 Have a look at the [[https://bcc2020.sched.com/event/coLw][video]] ([[https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing][alternative +link]]) and the [[https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing][poster]]. * Who created the public sequence resource? @@ -176,7 +210,7 @@ because we know people like the attribution clause. In all honesty: we prefer both data and software to be free. -* Are there also variant in the RDF databases? * +* Are there also variant in the RDF databases? We do output a RDF file with the pangenome built in, and you can parse it because it has variants implicitly. @@ -193,14 +227,23 @@ plan to combine identifiers with clinical data stored securely at We are planning to remove reads that match the human reference. -* Does PubSeq support only SARS-CoV-2 data? * +* Does PubSeq support only SARS-CoV-2 data? To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to be able to support other species in the future. * How do I communicate with you? -We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join. +We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join. See also [[./contact][contact]]. + +* Citing PubSeq + +We have two publications in the works. Until we have a DOI please cite +PubSeq in the following way: + +We made use of the COVID-19 public sequence (PubSeq) resources hosted +at http://covid19.genenetwork.org/. + * Who are the sponsors? |