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  • Oct 22 2018 21:12

    dimus on v4.0.3

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  • Oct 22 2018 21:12

    dimus on master

    v 4.0.3 gems update (compare)

  • Sep 18 2017 08:28

    dimus on v4.0.2

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  • Sep 18 2017 08:28

    dimus on master

    add span for resolution (compare)

  • Sep 17 2017 18:57

    dimus on master

    make rubocop happy (compare)

  • Sep 17 2017 14:24

    dimus on v4.0.1

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  • Sep 17 2017 14:24
    dimus closed #43
  • Sep 17 2017 14:24

    dimus on master

    Fix #43 partially The idea was… (compare)

  • Sep 14 2017 22:19

    dimus on 43-unify-resolution-injestion

    wip (compare)

  • Sep 14 2017 21:47

    dimus on 43-unify-resolution-injestion

    wip (compare)

  • Sep 13 2017 22:02

    dimus on 43-unify-resolution-injestion

    Fix #43 unify injection and res… (compare)

  • Sep 13 2017 21:30

    dimus on 43-unify-resolution-injestion

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  • Sep 13 2017 21:26
    dimus opened #43
  • Sep 13 2017 20:20

    dimus on v4.0.0

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  • Sep 13 2017 20:20

    dimus on 42-better-eta

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  • Sep 13 2017 20:20
    dimus closed #42
  • Sep 13 2017 20:20

    dimus on master

    Fix #42 - better speed estimati… (compare)

  • Sep 12 2017 22:16

    dimus on 42-better-eta

    wip (compare)

  • Sep 12 2017 21:46

    dimus on 40-concurrency

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  • Sep 12 2017 21:45

    dimus on 42-better-eta

    Fix #42 - better speed estimati… (compare)

Matthias Grenié
@Rekyt

Yes, I am @dimus 00 they are great tools! @Rekyt do you have a twitter account? May we loop you into our tweets?

Yes of course! My handle is @LeNematode

Dmitry Mozzherin
@dimus
I am wriging some info about gnparser as we speak, verifier will be next
So there will be updates at globalnames.org soon
thank you for another gentle push @Rekyt :)
Debbie Paul
@debpaul
Thank you @Rekyt -- great twitter handle!
Matthias Grenié
@Rekyt

Thank you @Rekyt -- great twitter handle!

Thanks!

Dmitry Mozzherin
@dimus
What makes Go a great language for biodiverstity informatics? https://globalnames.org/news/2021/07/14/go/
Debbie Paul
@debpaul
Cool! I'll at the very least > retweet your tweet. And I can loop in a few other groups / people on Twitter who might find this intriguing :-)
Dmitry Mozzherin
@dimus
Thanks @debpaul! I hope the post will be useful for someone who does need fast and simple language.
There is another interesting language https://vlang.io/ that tries to remove limitations in Go and Rust, but I won't trust it at this point of time.
Kaveh Karimi
@ka7eh
Hi and thanks for this great project! I recently started using Global Names tools for a project and noticed you have two organization accounts on Github: GlobalNamesArchitecture and gnames. Some repos like gnfinder exist in both places, though the ones on gnames account are more recent (I think?). What's the connection between the two accounts and which one is the main source?
Dmitry Mozzherin
@dimus
Hi @ka7eh github.com/GlobalNamesArchitecture mostly contains Ruby projects, all of them were done earlier. The `github.com/gnames' contains more recent implementations written in Go. The Go code is planned to be developed further, while Ruby code will be more and more deprecated/removed with time.
You can see https://globalnames.org for news, docs and tutorials. In general gnfinder, gnverifier, gnparser from gnames are the main projects that are actively developed now.
Amanda Lea Whitmire
@amandawhitmire
@dimus I can't seem to get GNfinder to work with URLs. Are there any known bugs for that option? I'm able to read text files without any issues. Am using the command line app. Thanks!
Dmitry Mozzherin
@dimus
@amandawhitmire what is your operating system? How about PDF files? Does gnfinder works for them?
Dmitry Mozzherin
@dimus
did you install GNfinder using brew?
I was one verision behind with brew, now I updated it to GNfinder v0.14.2, so if you did use brew try to install it again.
Amanda Lea Whitmire
@amandawhitmire
Hi @dimus - thank you! I'm on a Mac running Catalina, 10.15.7. I haven't tried PDFs (no need), but am happy to do that if it's helpful to you. I did use brew for the install. I'll install it again and let you know ASAP.
It works!! Awesome - thanks very much. I appreciate it!!
Matthias Grenié
@Rekyt
Hi @dimus :)
Thank you for all your great answers to my questions.
Because we're compiling databases for our review on taxonomic harmonization (see preprint here: https://ecoevorxiv.org/e3qnz/), we would be interested to know the global numbers of names indexed by GNIndex and GNResolver. With a break down between total number of names vs. accepted names vs. synonyms if possible.
Because we couldn't find these on the websites
Dmitry Mozzherin
@dimus
Hi @Rekyt, there are 33 million name-strings accumulated by GNverifier so far, but 6 millions of them are 'orphans' that dissapeared from data-sources with time. So only 27 million names are connected to current data-sources
accepted names/vs sysnonyms is a harder questions, because it it taxonomy, and as such depends on a source. For example in CoL there are 4 million name-strings for 2 million species
Dmitry Mozzherin
@dimus
In general in GNverifier database for 27 mil name-strings there are 8 million canonical forms. The last estimation for known species I heard was ~2.5 million. So I would estimate that for 2.5 million species there are ~8 million names and ~100 million name-strings "in the wild"
Dmitry Mozzherin
@dimus
@Rekyt, thank you for sharing link with your paper, looks like an interesting read
Matthias Grenié
@Rekyt
Thank you for the estimations, they give a good first idea of the issue with name-matching. So it's complicated from GNverifier to get the numbers for accepted species?
Dmitry Mozzherin
@dimus
I cannot wrap my head around how to do it well. Many resources are either nomenclatural, or even "lexical" and do not have any synonymy attached. Other resources are derivatives, for example GBIF accepted names are derivatives from Catalogue of Life whichh in turn takes data from, for example Index Fungorum, ITIS etc. Other resources are just plain dirty, like ION, and some are centuries old like Index Animalium. Then there is TreeOfLife who just slam together several classifications and end up with way more species than it is estimated. Then different nomenclatural codes have somewhat different approach and terms to what CoL calls an 'accepted name'. So I think such estimation can only be given "according to" a particular source, and in my opinion CoL puts more effor than other sources to compile a global, and manually curated approximation of such taxonomic data.
Matthias Grenié
@Rekyt
I understand now! Thanks for the details. This knowledge is invaluable expertise!
Dmitry Mozzherin
@dimus
I consider that there are 3 levels in biodiveersity: lexical, nomenclatural and taxonomical
image.png
GN tools, I think, are mostly about the lexical level
Katja Seltmann
@seltmann
@dimus I have a checklist of bees to add to global names. What is the best way to communicate about it? The names are in tsv & csv formats here https://zenodo.org/record/5738043
Dmitry Mozzherin
@dimus
Thanks @seltmann I'll add it to gn this month, I'll let you know if I have any trouble with import
Katja Seltmann
@seltmann
@dimus excellent, thank you.
Kaveh Karimi
@ka7eh
@dimus is there any way to adjust the log level for gnverifier (and other packages) through CLI? I looked at the docs and didn't see anything. I'm calling gnverifier from a python script, and the current log level interferes with my own logs and makes it hard to read.
I'm not familiar with Go, but looking at the docs for logrus, I think it should be an easy addition. If there's any interest in supporting a log level flag, I can work on a PR for it.
Dmitry Mozzherin
@dimus
yes it is an easy thing to add I am making a ticket gnames/gnverifier#70
there is such option for gnparser -q, I'll add the same to gnverifier. Log goes to STDERR, so redirecting STDERR to /dev/null would be enother way to solve it
Dmitry Mozzherin
@dimus
another way is to use either https://verifier.globalnames.org/api/v0 or /api/v1 directly (version 0 is the future v2), documenation is at https://apidoc.globalnames.org/gnames and https://apidoc.globalnames.org/gnames-beta
Kaveh Karimi
@ka7eh
Thanks, and good point about redirecting to /dev/null.
Dmitry Mozzherin
@dimus
@ka7eh GNverifier v0.6.3 has -q option
Kaveh Karimi
@ka7eh
Great! Thanks for the update.
Dmitry Mozzherin
@dimus
Tomorrow after 19:00 UTC we are going to do upgrade of kubernetes cluster, if all goes well, we will have GN down for a few minutes/half an hour.
Dmitry Mozzherin
@dimus
Kubernetes update is done, all should be back to normal
Dmitry Mozzherin
@dimus
Our network was down on university level for an hour or so, network and GN services are now restored
Archilegt
@Archilegt
Hi, Dima! Which is the repo of the gnparser in Go? I want to open the first issue for our paper.
Dmitry Mozzherin
@dimus
Hi Carlos, here it is https://github.com/gnames/gnparser
Archilegt
@Archilegt
Yaaay, thanks! :D