%title: How Big is That Bee? %author: https://jhpoelen.nl %date: 2023-03-28 -> How Big is That Bee? <- -> Jorrit Poelen @ Nano Session 2023-03-28 <- --------------------------------------------------- -> # Open Questions <- -> How to refer to *original* sources of trait data ? <- -> How to let biologists speak data in their native language: csv? <- -> How to translate native data speak into nanopubs? <- --------------------------------------------------- -> How Big is What Bee? <- --------------------------------------------------- -> How Big is UCSB-IZC00012194? <- --------------------------------------------------- -> The world is full of CSV <- -> The big picture: <- -> Even well into the 21st century, our world is full of text-formatted data like CSV. <- -> We need tooling to thrive in this world, nimbly manipulating data which is in CSVs. <- -> And we need tooling to move beyond CSV, <- -> to be able to pull data out and into other storage and processing systems. <- -> -- [Miller](https://miller.readthedocs.io/ accessed at 2023-03-28) <- --------------------------------------------------- -> The world of *biological trait measurement* is full of CSV <- -> Like Measurements of [Intertegular Span](Cane, J. H. 1987. Estimation of bee size using intertegular span Apoidea. J. Kansas Entomol. Soc. 60:145-147.) <- -> like those published by [Seltmann et al.](https://github.com/Big-Bee-Network/trait-intertegular-distance) <- -> including [UCSB-Microscope.csv](https://raw.githubusercontent.com/Big-Bee-Network/trait-intertegular-distance/main/UCSB-Microscope.csv) <- --------------------------------------------------- -> What (*not* where) biological trait measurements *exactly* ? <- -> Like Measurements of [Intertegular Span](Cane, J. H. 1987. Estimation of bee size using intertegular span Apoidea. J. Kansas Entomol. Soc. 60:145-147.) <- -> like those published by [Seltmann et al.](https://github.com/Big-Bee-Network/trait-intertegular-distance) <- -> including [UCSB-Microscope.csv](https://raw.githubusercontent.com/Big-Bee-Network/trait-intertegular-distance/main/UCSB-Microscope.csv) <- -> as identified by [hash://sha256/436ac4ec8a78c1cb86e9616b31b0c63bd76075e0551584a30f3ba73628c00723](https://linker.bio/hash://sha256/436ac4ec8a78c1cb86e9616b31b0c63bd76075e0551584a30f3ba73628c00723) . <- --------------------------------------------------- [body size of UCSB-IZC00012194](line:hash://sha256/436ac4ec8a78c1cb86e9616b31b0c63bd76075e0551584a30f3ba73628c00723!/L1,L7) ``` subject_id_NfN,catalogNumber,measurementType,measurementValue,measurementUnit,... ,UCSB-IZC00012194,body size;intertegular distance;ITD,65,mm,... ``` --------------------------------------------------- -> [give it a name: UCSB:IZC:UCSB-IZC00012194-itd.csv](preston alias UCSB:IZC:UCSB-IZC00012194-itd.csv 'line:hash://sha256/436ac4ec8a78c1cb86e9616b31b0c63bd76075e0551584a30f3ba73628c00723!/L1,L7') <- --------------------------------------------------- -> [body size of UCSB-IZC00012194](preston cat UCSB:IZC:UCSB-IZC00012194-itd.csv) <- ``` subject_id_NfN,catalogNumber,measurementType,measurementValue,measurementUnit,... ,UCSB-IZC00012194,body size;intertegular distance;ITD,65,mm,... ``` --------------------------------------------------- -> [body size of UCSB-IZC00012194](preston cat UCSB:IZC:UCSB-IZC00012194-itd.csv | mlr --icsv --oxtab cat) <- ``` catalogNumber UCSB-IZC00012194 measurementType body size;intertegular distance;ITD measurementValue 65 measurementUnit mm measurementDeterminedBy Katja Seltmann measurementDeterminedDate 2023-02-10 measurementMethod Measured under microscope measurementRemarks ``` ---------------------------------------------------- -> [body size of UCSB-IZC00012194](preston cat UCSB:IZC:UCSB-IZC00012194-itd.csv | np) <- ``` @prefix this: . @prefix sub: . @prefix np: . [...] sub:Head { this: np:hasAssertion sub:Assertion; np:hasProvenance sub:Provenance; np:hasPublicationInfo sub:Pubinfo; a np:Nanopublication . } sub:Assertion { [...] } ``` -------------------------------------------------- -> Which one would *you* choose? <-
-> [github:big-bee-network/traits-intertegular-span](https://github.com/big-bee-network/traits-intertegular-span) <-
-> [csv](https://raw.githubusercontent.com/Big-Bee-Network/trait-intertegular-distance/main/UCSB-Microscope.csv) <-
-> [csv](line:hash://sha256/436ac4ec8a78c1cb86e9616b31b0c63bd76075e0551584a30f3ba73628c00723!/L1,L7) <-
-> [xtab](preston cat UCSB:IZC:UCSB-IZC00012194-itd.csv | mlr --icsv --xtab cat) <-
-> [nanopub](preston cat UCSB:IZC:UCSB-IZC00012194-itd.csv | np) <- -------------------------------------------------- -> [traits of UCSB-IZC00012194](hash://sha256/96bfde1efa599e0e8e61de18b14d61dd308737f684950e4079c04e9bc0f33958) are described by many things: <- -> github repository, <- -> csv, <- -> csv, <- -> csv, <- -> xtab, <- -> nanopubs?, <- -> etc <- -------------------------------------------------- -> How did we package for re-use? <- -> Keep the Originals as Is <- -> Record Provenance Using [RDF/N-Quads Prov/PAV](https://preston.guoda.bio) <- -> Treat URLs as URLs <- -> [Use Content Ids to Reference Content](Elliott, MJ, Poelen, JH, & Fortes, J. 2023 in review. Signed Citations: Making Persistent and Verifiable Citations of Digital Scientific Content. https://doi.org/10.31222/osf.io/wycjn) <- -------------------------------------------------- -> Tools used: <- -> bash <- -> [preston](https://preston.guoda.bio) <- -> [miller](https://miller.readthedocs.io/) <- -------------------------------------------------- -> # Open Questions <- -> How to refer to *original* sources of trait data ? <- -> How to let biologists speak data in their native language: csv? <- -> How to translate native data speak into nanopubs? <- -------------------------------------------------- -> # Acknowledgements <- This work is partly supported by [Extending Anthophila research through image and trait digitization (Big-Bee)](https://big-bee.net) National Science Foundation Awards: 2102006, 2101929, 2101908, 2101876, 2101875, 2101851, 2101345, 2101913, 2101891 and 2101850.