BiCIKL roundtable on Wikidata and Molecular research by https://padlet.com/lauratilley3/n8g83tj59xyhdz9x en-us 2022-12-13 10:02:55 UTC 2022-12-16 16:01:42 UTC hello@padlet.com Microbial phenotypes https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423113774 To explore to cover phenotypic information]]> 2022-12-16 15:13:56 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423113774 Yes https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423114418 To disambiguate people and link them to their publications]]> 2022-12-16 15:14:24 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423114418 often https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423114859 For referencing people, things, place etc. ]]> 2022-12-16 15:14:50 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423114859 Yes https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423115627 Curating scientific authors of interest, plus other Biodiversity related data. ]]> 2022-12-16 15:15:38 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423115627 Teaching SPARQL and Linked Data concepts https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423115728 2022-12-16 15:15:45 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423115728 Cached Synchrony https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423116430 I use wikidata as the source of information about collectors of biological specimens. I use a ruby-based client, which calls the SPARQL endpoint. The flavour of these can be characterized by: "What is new in wikidata that I was unaware of?" and "What is changed in wikidata for the items I care about since the last time I checked?"]]> 2022-12-16 15:16:26 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423116430 extending the shared knowledge that we use as a platform for our research https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423116728 2022-12-16 15:16:43 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423116728 Reconciliation of new datasets https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117085 Used in onto refine to translate datasets values to Wikidata urls]]> 2022-12-16 15:17:04 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117085 Genomes https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117117 WD could be used (more) to link to multiple genome related data and concepts e.g. Reference genomes, representative genomes, genome publications, Pan-genomes etc etc]]> 2022-12-16 15:17:06 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117117 biological pathways https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117233 understanding the substrates and products of enzymic reactions]]> 2022-12-16 15:17:13 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117233 Molecular pathways across taxa https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117441 Querying across taxa to find pathways completed by multiple taxa in complex symbioses (e.g. lichens)]]> 2022-12-16 15:17:23 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117441 Unified reference database https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117506 we know we talk about the same things, when we reference them by their WD-id]]> 2022-12-16 15:17:27 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117506 Yes, as inspiration or critical mass of data in linked data approaches https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117535 2022-12-16 15:17:28 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117535 Sample information https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117950 Genomes are often obtained from samples with specific information, location, conditions.]]> 2022-12-16 15:17:53 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423117950 biotic interactions https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423118519 2022-12-16 15:18:22 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423118519 That's a big question! https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423118563 Wikidata is clearly not the only linked data store where we could collaborate]]> 2022-12-16 15:18:23 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423118563 Wikibase network https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423119139 Many of the topics mentioned could "blow up" Wikidata, explore distributed wiki bases? ]]> 2022-12-16 15:18:56 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423119139 Taxonomy seems like a common need https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423119856 2022-12-16 15:19:38 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423119856 General standardisation https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423120008 2022-12-16 15:19:48 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423120008 Source of bulk aggregated data https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423120051 Use data dumps to collate data - find it too easy to write queries that timeout on the web interface]]> 2022-12-16 15:19:51 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423120051 Semantic Integration https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423120093 As a key integrator of disparate sources of data, provided members of each stakeholder community have agreed upon their key concepts/integrators. If these are unknown at present then properties should be proposed to the wikidata community to facilitate that integration.]]> 2022-12-16 15:19:53 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423120093 Identify missing wikipedia articles on taxa https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423120907 2022-12-16 15:20:39 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423120907 Map GBIF and iNaturalist identifiers https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121108 2022-12-16 15:20:52 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121108 New tools https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121340 Develop tools for improved addition of new items for articles or books using DOIs or ISBN numbers. Maybe could be an add-on for cradle, where some of the properties are automatically populated using a supplied ISBN etc?]]> 2022-12-16 15:21:10 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121340 Translate database terms into many languages https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121632 2022-12-16 15:21:29 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121632 Tooling https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121835 Many applications are focused on Wikidata but wikibase support is not always there or not clear.]]> 2022-12-16 15:21:42 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121835 Make it simpler to get an overview of a given topic https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121961 2022-12-16 15:21:50 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423121961 Several suggestions in the bottom section of the Google doc https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423123332 2022-12-16 15:23:04 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423123332 As a source of bibliographic data that can be used for sciencometrics https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423123665 This also makes it easier to actually provide reference information, so as to support detailed provenance.]]> 2022-12-16 15:23:27 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423123665 Standardized information about type specimens https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423123745 2022-12-16 15:23:31 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423123745 Sensitive data about people https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423124048 2022-12-16 15:23:52 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423124048 Give Shape to the Landscape https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423124232 Define the key items & what are their expected properties. If these are lacking in wikidata, create/launch a consortium of stakeholders & involve wikidata admins in the process who will be sensitive to scalability.]]> 2022-12-16 15:24:04 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423124232 Re: Tooling https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423124570 But is has gotten a lot better in the last year(s). There is a lot of activity by the Wikidata/Wikibase - Team of Wikimedia with the focus on wikibase.]]> 2022-12-16 15:24:27 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423124570 Not sure https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423124933 All species (metadata) and genome (metadata) in an instance]]> 2022-12-16 15:24:48 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423124933 Many traits of organisms https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423125244 2022-12-16 15:25:09 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423125244 Standardized information about species distributions (or even molecularly characterized populations) https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423125572 With key parameters being 
- time frame
- native vs. introduced vs. invasive
- determination method]]> 2022-12-16 15:25:33 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423125572 community editing https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423126841 Planning databases to collate taxon metadata. Community editing tools would be good - Likely a wiki base instance as it sounds like incorporating all needed new ontology terms into main Wikidata may take longer than funding cycle]]> 2022-12-16 15:26:54 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423126841 Entity Explosion: https://www.wikidata.org/wiki/Wikidata:Entity_Explosion https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423126906 2022-12-16 15:26:59 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423126906 Make more ontologies and datasets CC0 https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423127119 2022-12-16 15:27:15 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423127119 sciencestories https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423127457 http://www.sciencestories.io/]]> 2022-12-16 15:27:37 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423127457 Integrating a workflow with Wikidata provides an avenue to make that workflow (more) FAIR. https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423127772 2022-12-16 15:27:46 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423127772 https://twitter.com/pigsonthewing/status/867270004017909760 https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423128302 2022-12-16 15:28:16 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423128302 Patient data https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423128755 2022-12-16 15:28:45 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423128755 All of X https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423128801 with X being specimens, sequences, supernovae etc.

Wikidata has a way to state that as "always incomplete"]]> 2022-12-16 15:28:48 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423128801 Endangered species https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423128993 Poachers read open data too

]]> 2022-12-16 15:29:01 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423128993 Federate usage beyond Wikidata and Wikibase https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423130692 Create a linked data landscape that spreads accross Wikidata/Wikibase on one side and other triple store on others

]]> 2022-12-16 15:30:33 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423130692 How deep do you go? https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423130982 A frontend script *could* call wikidata in real-time, which puts strain on the wikidata infrastructure. But, one could also plan for an arm's length cache and resync. The former might be fruitful for a quick proof-of-concept, but as a project matures, the latter could be desirable.]]> 2022-12-16 15:30:54 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423130982 Positive feedback loops between mining/entity recognition workflows and Wikidata https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423131000 2022-12-16 15:30:55 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423131000 Granularity is an issue https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423133421 e.g. some databases take into account stereochemistry (and Wikidata can do that too) but many others don't, which raises mapping issues known as the "Bonnie and Clyde problem" https://meta.wikimedia.org/wiki/Community_Wishlist_Survey_2019/Wikidata/Solution_to_the_%E2%80%9FBonnie_and_Clyde%E2%80%9D_problem]]> 2022-12-16 15:33:13 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423133421 The mess from linking helps make the problems obvious https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423134233 2022-12-16 15:33:57 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423134233 Some visualizations/ maintenance queries can reveal data quality issues https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423135475 e.g. localities of high-altitude specimens that are in the middle of the ocean due to some formatting mishap with the geodata]]> 2022-12-16 15:35:11 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423135475 Lots of the Wikidata tools are effectively serving as citizen science projects https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423136440 2022-12-16 15:36:10 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423136440 BiCIKL-type infrastructures could provide mirrors of Wikidata https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423157917 perhaps with different specs, e.g. trading higher execution times for lower update frequencies and such]]> 2022-12-16 15:55:33 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423157917 The ethics of profiling people and other entities in such a public place have not yet been explored comprehensively https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423162400 2022-12-16 15:59:56 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423162400 Natural product data https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423164256 e.g. as per https://doi.org/10.7554/eLife.70780]]> 2022-12-16 16:01:42 UTC https://padlet.com/lauratilley3/n8g83tj59xyhdz9x/wish/2423164256