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Blogpost for GenR and FORCE11
I would like to put out one or more blogposts about openVirus. The first with the angle of innovating Open Science systems in relationship to COVID-19. This is for GenR a blog I edit and we are running a theme along these lines, the blogpost can also be posted on FORCE11 as there is an invitation to do this. See GenR theme call: https://genr.eu/wp/covid-19-and-innovating-open-science-systems/
The idea is that this a post open to all on openVirus.
I need to do this first one quite quickly as there are two online conferences next week. So want to publish Tuesday 23 before 10am CEST.
But we can do more, and of different lengths.
- Collect ideas for blog post
- Write blog post - word length of 800 words is good
- Review blog post
- Publish
- What is the overall innovation and then some specific examples
- Describe the openVirus project
- Give a timeline and motivation
- Invitation to get involved
- Include the mini project - https://github.com/petermr/openVirus/tree/master/miniproject
- bioRxiv in Citizen Health Search (CHS)? - can this be used.
openVirus - Scientific Knowledge for citizens in the time of COVID. A new knowledgebase by/for citizens.
'The software will demonstrate how we can search in future'
The Ebola paper: A serological survey on viral haemorrhagic fevers in liberia - https://doi.org/10.1016/S0769-2617(82)80028-2, 1982
Ebola, Liberia
Explain what openVirus does:
Mining:
- build scrapers or API query tools for Openly readable sources.
- query or scrape user questions
- download raw content (PDF, HTML, images) - 10 - 10,000 articles
- clean and semantify
- annotate with dictionaries
- expose, analyze, display
tools:
- framework: ami + CProject data
- scrapers: getpapers, Ferret, curl, scrapy
- cleaners: PDFBox, Tidy/Jsoup, etc. Grobid
- transformers: xml2html, ami ocr, KNIME
- dictionaries: ami dictionary
- indexing and annotation: Solr, ami
- Analysis and display: R, KNIME
Sources: EuropePMC, biorxiv and medrxiv, DOAJ, EThOS, Redalyc (MX)
Join us! Testers, graphics, software, queries, scraper, and documenting.
Upload previous presentation slides to Zenodo COVID community - currently offline 20.6 https://zenodo.org/communities/covid-19/
- EU Virus hack
- Pubfest
- Summer school