[Wikidata-l] Tree Of Life

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Lucie Kaffee

18 Dec 2014 18 Dec '14

4:35 p.m.

Hey, Since the Tree of Life by Denny is outdated, we thought it was a nice idea, to have a new one, to have an overview over the biological taxonomy on wikidata. Not only to have a nice looking tree but also to see, where errors are and to correct and update it. Right now, there are 660775 Items in the tree. Even though the change of names can be seen instantly, because this is based on the API, changes in the order need an update of the whole tree, because it's based on wikidata dumps. (This one on the most recent one from 15.12.2014) Here you go, this is the new tree of life, made with a lot of love: https://tools.wmflabs.org/tree-of-life/ If you have any corrections, additions or features you want to add, feel free to ping me, send me a mail, submit a patch or file an issue on github. The repo for the tree is on https://github.com/frimelle/tree-of-life Cheers, Lucie (frimelle)

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Gregor Hagedorn

18 Dec 18 Dec

7:38 p.m.

https://tools.wmflabs.org/tree-of-life/ is problematic at first looks. Bacteria, prokaryotes, monera and eukaryoates as sister groups on the same level? Prokaryotes contain as only subtaxon Archaea (but no bacteria)? Also, the mixed use of scientific and common names (variously as singular or plural) is rather confusing. sorry for the critique... gregor On 18 December 2014 at 17:35, Lucie Kaffee <lucie.kaffee(a)wikimedia.de> wrote:

...

-- --------------------------------- Dr. G. Hagedorn +49 (0)30 2093 8576 (work) +49-(0)30-831 5785 (private) gregor.hagedorn(a)mfn-berlin.de http://www.linkedin.com/in/gregorhagedorn This communication, together with any attachments, is made entirely on my own behalf and in no way should be deemed to express official positions of my employer. It is intended only for the person(s) to whom it is addressed. Redistributing or publishing it without permission may be a violation of copyright or privacy rights.

Lydia Pintscher

7:52 p.m.

On Thu, Dec 18, 2014 at 8:38 PM, Gregor Hagedorn <g.m.hagedorn(a)gmail.com> wrote:

...

Hey Gregor, That's exactly why Lucie made the tool ;-) It is only a reflection of the data in Wikidata. So if it is wrong in the tree it is wrong in Wikidata and should be fixed. Cheers Lydia -- Lydia Pintscher - http://about.me/lydia.pintscher Product Manager for Wikidata Wikimedia Deutschland e.V. Tempelhofer Ufer 23-24 10963 Berlin www.wikimedia.de Wikimedia Deutschland - Gesellschaft zur Förderung Freien Wissens e. V. Eingetragen im Vereinsregister des Amtsgerichts Berlin-Charlottenburg unter der Nummer 23855 Nz. Als gemeinnützig anerkannt durch das Finanzamt für Körperschaften I Berlin, Steuernummer 27/681/51985.

Gregor Hagedorn

19 Dec 19 Dec

9:33 a.m.

Thanks Lydia, agreed, the tool absolutely is useful and many thanks to you, Lucie and your team, for providing it!!!! However, it is difficult for me to say what needs to be resolved on the tools level and what on Wikidata content. What I observe looks to me (but I may be wrong) a mashup-error occurring when uncritically combining data from different sources, each source being internally consistent and correct. This may be something that needs to be addressed by the tool. The problem with different labels and singular/plural may or may not be a tool problem in choosing the correct label One problem I have when using the tool to try to understand what is going on: It should variously wikidata and wikipedia pages, making it somewhat difficult to follow what goes on. E.g. Biota is a wikidata page, bacteria is a wikipedia page... So again thanks for doing this great work! gregor On 18 December 2014 at 20:52, Lydia Pintscher <lydia.pintscher(a)wikimedia.de> wrote:

...

On Thu, Dec 18, 2014 at 8:38 PM, Gregor Hagedorn <g.m.hagedorn(a)gmail.com> wrote:

https://tools.wmflabs.org/tree-of-life/ is problematic at first looks. Bacteria, prokaryotes, monera and eukaryoates as sister groups on the

same

level? Prokaryotes contain as only subtaxon Archaea (but no bacteria)? Also, the mixed use of scientific and common names (variously as

singular or

plural) is rather confusing. sorry for the critique...

-- --------------------------- Dr. Gregor Hagedorn Head of Digital World and Information Science Museum für Naturkunde Berlin Leibniz-Institut für Evolutions- und Biodiversitätsforschung Invalidenstrasse 43, 10115 Berlin +49 (0)30 2093 8576 (work) +49-(0)30-831 5785 (private) gregor.hagedorn(a)mfn-berlin.de http://www.naturkundemuseum-berlin.de http://linkedin.com/in/gregorhagedorn This communication, together with any attachments, is intended only for the person(s) to whom it is addressed. Redistributing or publishing it without permission may be a violation of copyright or privacy rights. Halloween = Christmas? 31 Oct = 25 Dec!

Lydia Pintscher

10:22 a.m.

Hey Gregor, On Fri, Dec 19, 2014 at 10:33 AM, Gregor Hagedorn <gregor.hagedorn(a)mfn-berlin.de> wrote:

...

Good point, yes. Any ideas how?

...

The problem with different labels and singular/plural may or may not be a tool problem in choosing the correct label

It just takes the label of the item. There is a taxon name property. Would that be a useful alternative? Input from the experts needed.

...

One problem I have when using the tool to try to understand what is going on: It should variously wikidata and wikipedia pages, making it somewhat difficult to follow what goes on. E.g. Biota is a wikidata page, bacteria is a wikipedia page...

Right. It shows the Wikipedia article if there is one in the language you selected and otherwise Wikidata. Better to always show Wikidata?

...

So again thanks for doing this great work!

All thanks go to Lucie ;-) Cheers Lydia -- Lydia Pintscher - http://about.me/lydia.pintscher Product Manager for Wikidata Wikimedia Deutschland e.V. Tempelhofer Ufer 23-24 10963 Berlin www.wikimedia.de Wikimedia Deutschland - Gesellschaft zur Förderung Freien Wissens e. V. Eingetragen im Vereinsregister des Amtsgerichts Berlin-Charlottenburg unter der Nummer 23855 Nz. Als gemeinnützig anerkannt durch das Finanzamt für Körperschaften I Berlin, Steuernummer 27/681/51985.

Gregor Hagedorn

1:25 p.m.

...

may be wrong) a mashup-error occurring when uncritically combining data

from

different sources, each source being internally consistent and correct.

This

may be something that needs to be addressed by the tool.

Good point, yes. Any ideas how?

Perhaps just help understanding this better, by displaying the sources for the relations shown

...

The problem with different labels and singular/plural may or may not be a tool problem in choosing the correct label

It just takes the label of the item. There is a taxon name property. Would that be a useful alternative? Input from the experts needed.

That seems helpful. One way would be to always show taxon name first, followed by the - at the moment perhaps inconsistent - language label in Parentheses

...

Right. It shows the Wikipedia article if there is one in the language you selected and otherwise Wikidata. Better to always show Wikidata?

perhaps iframe with the mobile-view as it is PLUS 2 normal (quick-) links below, allowing to open the normal-view pages to conveniently analyse/ read etc. ... not sure. Situation at the moment is that when I tried to understand the source of the mashup error, I could not do it with the information or links displays thanks again gregor

Lucie Kaffee

1:52 p.m.

2014-12-19 14:25 GMT+01:00 Gregor Hagedorn <gregor.hagedorn(a)mfn-berlin.de>de>:

...

may be wrong) a mashup-error occurring when uncritically combining data from

different sources, each source being internally consistent and correct.

This

may be something that needs to be addressed by the tool.

Good point, yes. Any ideas how?

Perhaps just help understanding this better, by displaying the sources for the relations shown

The problem with different labels and singular/plural may or may not be

tool problem in choosing the correct label

It just takes the label of the item. There is a taxon name property. Would that be a useful alternative? Input from the experts needed.

That seems helpful. One way would be to always show taxon name first, followed by the - at the moment perhaps inconsistent - language label in Parentheses

I will have a look at this, but it shouldn't be a big issue to change this!

...

Right. It shows the Wikipedia article if there is one in the language you selected and otherwise Wikidata. Better to always show Wikidata?

Links to wikidata and wikipedia shouldn't be a problem either. I will have a look into that the next days! Would that help for the first point, too?

...

thanks again

Very welcome! Thank you for your comments :) Lucie

...

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Magnus Manske

23 Dec 23 Dec

5:41 p.m.

Little late to the party, but I feel I need to say: great work Lucie! On Fri, Dec 19, 2014 at 2:52 PM, Lucie Kaffee <lucie.kaffee(a)wikimedia.de> wrote:

...

2014-12-19 14:25 GMT+01:00 Gregor Hagedorn <gregor.hagedorn(a)mfn-berlin.de> :

may be wrong) a mashup-error occurring when uncritically combining data from

different sources, each source being internally consistent and

correct. This

may be something that needs to be addressed by the tool.

Good point, yes. Any ideas how?

Perhaps just help understanding this better, by displaying the sources for the relations shown

The problem with different labels and singular/plural may or may not

be a

tool problem in choosing the correct label

It just takes the label of the item. There is a taxon name property. Would that be a useful alternative? Input from the experts needed.

That seems helpful. One way would be to always show taxon name first, followed by the - at the moment perhaps inconsistent - language label in Parentheses

I will have a look at this, but it shouldn't be a big issue to change this!

Right. It shows the Wikipedia article if there is one in the language you selected and otherwise Wikidata. Better to always show Wikidata?

Links to wikidata and wikipedia shouldn't be a problem either. I will have a look into that the next days! Would that help for the first point, too?

thanks again

Very welcome! Thank you for your comments :) Lucie

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Gregor Hagedorn
Gregor Hagedorn
Lucie Kaffee
Lydia Pintscher
Magnus Manske