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\nWP4846 that I started on March 16. It will see a massive overhaul in the next weeks.
Voices are getting stronger over how important Open Science\nis. Insiders have known the advantages for decades. We also know the issues in the transition, but the transition has been steady. Contributing to Open Science is\nsimple: there are plenty of project where you can contribute without jeopardizing your own research (funding or prestige). Myself, my small contributions have been\ndone without funding too. But I needed to do something. I have been mostly self-quarantined since March 6,\nwith only very few exception. And I’m so done with it. Like so many other people. It won’t stop me wearing masks when I go shopping (etc).
\n\nReflecting on the past eight months, particularly the last two months have been tough. It’s easier to sit at home and in the garden when it is warm outside, light. But for another 7 weeks or so, they days will only get darker. The past two months were also so busy with grant reporting that I did not get around to much else, even with an uncommon long stretch of long working weeks, with about 8 weeks of 70-80 hrs of active work in that period. In fact, the past two weeks, with most of the deadlines past, I had a physical reset, and was happy if I made 40 hrs a week.
\n\nSo, where is my COVID-19 work now, where is it going?
\n\nFirst, what did we reach? First, leveraging from the Open Science community I am involved in, I stared collaborating. With old friends and making new\nfriends. I was delighted to see I was not the only one. In fact, Somewhere in May/June, I had to give up following all Open Science around COVID-19,\nbecause there was too much.
\n\nFor example, I was not the only one wanting to describe our slowly developing molecular knowledge of the\nSARS-CoV-2 virus. While my pathway focused on specifically the confirmed processes for SARS-CoV-2,\nmy colleague Freddie digitized a recent review about other corona viruses. Check out her work:\nWP4863, WP4864,\nWP4877, WP4880,\nand WP4912. In fact, In fact, so much was done by so many people in such a short time, that the\nWikiPathways COVID-19 Portal was set up.
\n\nFurther reading:
\n![](\"/assets/images/Screenshot_20201031_104646.png\")
Because I see an essential role for\nWikidata in Open Science, and because regular databases did not provide identifiers for the molecular building blocks,\nwe created them in Wikidata. This was essential, because I wanted to use Scholia (see screenshot on the\nright) to track the research output (something that by now has become quite a challenge; btw, checkout\nLauren’s tutorial on this). This too was\nstill in March. However, because Scholia itself is a\ngeneral tool, I needed shortlists of all SARS-CoV-2 genes, all proteins, etc. So, I created this book.\nIt’s autogenerated and auto-updated by taking advantage of SPARQL queries against Wikidata. And I am so excited the book has been translated in\nJapanese, Portugues, and\nSpanish. The i18n work is thanks to the\nvirtual BioHackathon in April, where Yayamamo bootstrapped the framework\nto localize the content.
\n\nAlso during that BioHackathon, we started a collaboration with Complex Portal’s\nBirgit, because the next step was to have identifiers for (bio)molecular complexes. This work is still ongoing, but using a\nworkaround we developed for WikiPathways (because complexes in GPML currently cannot have\nidentifiers), we can now link out to Complex Portal, as visible in this screenshot:
\n\n![\"\"](\"/assets/images/Screenshot_20200408_235320.png\")
Joining the Wikidata effort is simple. Just visit Wikidata:WikiProject_COVID-19\nand find your thing of interest. Because the past two months have been so crowded, I still did not get around to explore the\nkg-covid-19 project, but sounds very interesting too!
\n\nFurther reading:
\nFor some years now, I have been working on computer-assisted data curation of WikiPathways, but also Wikidata (for chemical compounds).\nOnce your biological knowledge is machine readable, you can have learn machines to recognize common mistakes. Some are basically\nsimple checks, like missing information. But it gets exciting if we take advantage of linked data, and we can have machines check\nconsistency between two or more resources. The better out annotation, the more powerful this computer-assisted data curation becomes.\nChris has been urging me to publish this, but I haven’t gotten around to this yet.
\n\nAs part of my COVID-19 work, I have started making curation reports for specific WikiPathways.\nTo enable this, I worked out how to reuse the testing without JUnit, allowing the tests to be used as a library. That allows creating the reports, but in the future\nwill also allow use directly in PathVisio. A second improvement to the testing stack is that tests are now more easily annotated.\nThat allows specifying tests only to be run for a certain WikiPathways portal.
\n\nBut a lot remains to be done. I think at this moment I only migrated, perhaps, some 5% of all tests. So, this is very much on my “what is next?” list.
\n\nThere is a lot I need, want, and should do. here are some ideas. Maybe you wan to beat me to it. Really, I don’t mind being scooped,\nwhen it comes to public health. Here goes:
\n\nAm I missing anything? Tweet me or leave a comment here.
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