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I was not there. I only joined the WikiPathways project in late 2011, just as a contributor.\nAnd it was just before joining the\nBiGCaT research team of Prof. Chris Evelo in January 2012,\nwhere I started a project in the Open PHACTS project, not really about WikiPathways,\nbut the open science WikiPathways was the main reason for me to join the group. Open PHACTS was close to my research and\njust created that opportunity.
\n\nWikiPathways was already around five years old when I created my account. It was created in January 2007\n(doi:10.1038/npre.2010.5361.1). It was first formally published in 2008\n(doi:10.1371/journal.pbio.0060184), so the project is about 20 years\nold (maybe a new WikiPathways conference next year?). The launch made it to Science\n(doi:10.1126/science.321.5889.623c):
\n\n\n\n\nThe makers of GenMAPP [..] have launched a site for\nsharing findings on metabolic pathways. [..]\nWikiPathways (wikipathways.org) offers a way to integrate\ninformation on these complex networks [..]\nThe site has more than 300 registered users and contains\ninformation on 500 metabolic pathways in seven species,\nincluding humans.
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And Nature (doi:10.1038/455022A):
\n\n\n\n\nAlexander Pico remembers just when the idea hit him. In January 2007, he and his boss, Bruce Conklin, were discussing\nhow to push their software tool for visualizing intracellular signalling pathways to the next level of interactivity —\nwhen Pico blurted out, “What we really need is a wiki!”
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Just like review article curate and put primary literature in context, so that WikiPathways.\nThey pitched it at the time as modelled after Wikipedia, but surely it is also just as well modelled\nafter traditional knowledge dissemination approaches. One can easily argue that the wiki approach is\nessential: anyone can create an account. And this has been held against WikiPathways. But if you look\nat the who actually edits WikiPathways, these are only people working in an academic research\nenvironment.
\n\nWikiPathways is, of course, used as a reference knowledgebase, and the use in pathway enrichment and\nnetworking approaches are perhaps the best known. Another aspect of a wiki, however, is the community approach:\na community can work out a collection of machine-readable (FAIR) pathway models, even when the discovery is in full swing.\nWikiPathways is also a platform to exchange knowledge, discuss literature, do research. The use to of\nthis feature turned out really useful at the start of the COVID-19 pandemic.
\n\nThe set of full genome assemblies was not that large; in 2021 there were 3278 genome assemblies for animal species\n(doi:10.1073/pnas.2109019118 and the Genomes on a Tree\n(doi:10.12688/wellcomeopenres.18658.1) reports 27883 assemblies\nfor 664 complete genomes.
\n\nFor WikiPathways, seven species in 2008 grew to 39 species today today,\nthough many of them only have a few curated pathways. Indeed, human is still the predominent species, in number of\npathways (visualized with this SPARQL query).
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That said, several communities have worked in the past to create\nsets of pathways\naround specific species. In that post, I already mentioned Wormbase, but we also have a collection of pathways\nfrom YeastPathways (doi:10.1093/genetics/iyae185),\nfor example wikipathways:WP137.\nNow, the yeast pathways are not in sync with the upstream SDG YeastPathways, I think, so there is some\ncuration to do on our side (from the 2025 Genetics paper):
\n\n\n\n\nAs the first major update since 2012, we updated 62 pathways with expert summaries on\npathway genetics, biochemistry, regulation, and more. Thirty-three new pathways with\nspecificity for yeast biochemistry were propagated from MetaCyc at SRI (Caspi et al. 2018),\nand 105 existing pathways were edited for proper enzymatic classification, reaction\nconnectivity, and gene attribution. Compounds that were previously missing a chemical\nstructure have also now been updated, along with the stoichiometry and scheme of many\npathway reactions.
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In similar style, WikiPathways has had similar project around setting up a pathway collection\nfor a new species, like cow in a project by Zahra Roudbari\n(doi:10.3389/fgene.2019.01370).\nAnd more recently atlantic cod\n(ongoing research by Madhushri S. Varunjikar\nfrom the Norwegian Institute of Marine Research).
\n\nBut WikiPathays also has a feature to convert pathways from one species to another. With more and\nmore whole genome assemblies becoming available, so are mappings of genes between one species and\nanother. This is the basis of that cow project (from the article):
\n\n\n\n\nThe online biological pathway repository, WikiPathways (Slenter et al., 2017), contains pathways\nof different species, however a B. taurus collection was missing.
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And:
\n\n\n\n\nSecond, the WikiPathways homology based the homology mapper which is available at GitHub\n(https://github.com/PathVisio/homology.mapper) was updated to improve homology coverage for gene\nproducts that were annotated with different data sources. The pathways were converted from human\npathways, with a required minimum successful conversion of at least 50% of the original human genes.
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The question is, of course, what is the best model species to use. That decision can be based on\nmultiple aspect, including the use case. There is freedom.
\n\nSo, when this week the book chapter Xenbase: A Guide to the Xenopus Genetics and Genomics Knowledgebase\nwas published (doi:10.1007/978-1-0716-5360-9_3), and\nI was pinged WikiPathways was cited, I started reading.
\n\n\n\n\nWikiPathways are linked via gene symbol (Fig. 6A, black arrow) link redirects to a pre-set gene\nsymbol search on this community-curated open science resource [20].
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The linking via gene symbol made me write up this post. If they have the mappings, then with\nthe GPML Homology Mapper we can create pathways\nfor the two frog species (X. laevis and X. tropicalis).
\n\nAnd there are reasons to do that. WikiPathways allows you to cite literature, at a pathway level,\nfor a gene, protein, or metabolite, and even at the level of an interaction. That literature is\nspecies specific. The curation can also work out what to do with those parts of pathways for\nwhich no genes were mapped. Having this is machine-readable knowledge has shown to be of\ngreat usability, at the very least making the knowledge much, much easier to find.
\n\nAnd that brings us back to another role of review articles, of book chapters giving expert overviews,\nbut also of wiki’s: put knowledge in perspective of the literature from which it is derived.\nI wish pathways database, generally, are used to communicate and get peer reviewed the fruits\nof the work studying the biological processes on all these species.
\n\nWith more than 600 full genomes and 39 species in WikiPathays, we have an exciting and growing seed.
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