species-brainstorming - Revision history

Barnabywalters: Added inactive template per discussion in IRC

2021-04-28T17:17:00Z

Added inactive template per discussion in IRC

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			{{inactive}}

	=Species Brainstorming=		=Species Brainstorming=

Kaldari: 3 comments

2010-03-22T15:44:00Z

3 comments

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	:[[User:AndyMabbett\|Andy Mabbett]] 14:42, 28 Feb 2007 (PST)		:[[User:AndyMabbett\|Andy Mabbett]] 14:42, 28 Feb 2007 (PST)

			==Ryan Kaldari==
			1. The name of this microformat needs to be changed ASAP. Calling it "species" is confusing and misleading. There was even resistance to implementing this microformat in Wikipedia solely because of the confusing name.[http://en.wikipedia.org/wiki/Template_talk:Taxobox#Hidden_microformat_category]

			2. Synonyms should be added as a node to the format.

			3. I wouldn't worry too much about accommodating LSIDs specifically, as it seems to be a rapidly dying format. Just concentrate on accommodating GUIDs in general (of any format) and identifying them as such. Also, keep in mind that many objects are going to have more than one GUID (even though this is discouraged), so we should be able to accommodate this.

	== Other use cases ==		== Other use cases ==

Brian: Reverted edits by LizelRobas (Talk) to last version by PeterR

2009-01-03T19:43:14Z

Reverted edits by LizelRobas (Talk) to last version by PeterR

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	~~boololeton~~
	=Species Brainstorming=		=Species Brainstorming=

LizelRobas: troccao

2009-01-03T18:40:02Z

troccao

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			boololeton
	=Species Brainstorming=		=Species Brainstorming=

PeterR: /* Species Brainstorming */

2008-02-21T22:18:55Z

Species Brainstorming

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	:'''Note: the original name of the proposed microformat, "species", is likely to change, probably to "biota" or "taxon". The former has been retained here, to avoid having to make many repetitive and perhaps redundant edits'''		:'''Note: the original name of the proposed microformat, "species", is likely to change, probably to "biota" or "taxon". The former has been retained here, to avoid having to make many repetitive and perhaps redundant edits'''

	:'''{{UpdateMarker} The [http://www.kaply.com/weblog/2007/02/16/operator-07a-is-available/ Operator] extension now detects ''Species''. [http://www.westmidlandbirdclub.com/records/lists-2004uf.htm A test page is available]. Work on both continues!'''		:'''{{UpdateMarker}} The [http://www.kaply.com/weblog/2007/02/16/operator-07a-is-available/ Operator] extension now detects ''Species''. [http://www.westmidlandbirdclub.com/records/lists-2004uf.htm A test page is available]. Work on both continues!'''

	==Andy Mabbett==		==Andy Mabbett==

AndyMabbett: sub-dividing

2008-01-17T09:13:11Z

sub-dividing

Show changes

RogerHyam: /* Taxonomic Databases Working Group */

2007-11-05T16:12:01Z

Taxonomic Databases Working Group

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	===Taxonomic Databases Working Group===		===Taxonomic Databases Working Group===

	[http://www.tdwg.org/index.html TDWG] is the organisation for standardisation in exchange of biodiversity data. The organisation ~~is currently undergoing a degree of~~ re-~~organisation~~ and ~~is developing an architecture to integrate the different standards~~ it ~~produces with each other and~~ with ~~those in use~~ in the ~~semantic web~~ and ~~geospatial communities. Part of this architecture will be a central ontology for things like scientific biological names~~.		[http://www.tdwg.org/index.html TDWG] is the organisation for standardisation in exchange of biodiversity data. The organisation has now (November 2007) undergone some re-organization. It has a new collaborative development environment, standards process, standards architecture and it has formed alliances with major organizations in the domains of geospatial and ecological data.

	~~Because of its role in bridging technologies~~ the ~~application that manages~~ the ~~ontology will need~~ to ~~be able to express~~ the ~~same basic semantics~~ in ~~multiple formats (e~~.g. ~~RDFS, OWL, Geography Mark Up, OBO etc)~~. ~~It seems logical that this application should also generate basic microformat definitions for each~~ of the ~~classes it contains. If we have an~~ ontology ~~defining 'Taxon Name' and 'specific epithet'~~ for ~~example~~ the ~~same notion should~~ be ~~mapped to~~ as ~~many~~ technologies as ~~possible~~.		Central to the TDWG standards architecture are the [http://wiki.tdwg.org/twiki/bin/view/TAG/LsidVocs LSID vocabularies]. The role of these vocabularies is to define URIs for the nuts-and-bolts concepts that occur in the biodiversity informatics domain. See [http://wiki.tdwg.org/twiki/bin/view/TAG/WhatIsTheOntology a description of what the TDWG ontology is] for details. Although the vocabularies are defined in OWL the intention is for their URIs to be used as namespaces across different XML and non-XML based technologies. They can act as a central mapping point for those hard pressed developers who want to combine data presented to them in many formats.

	TDWG is ~~also supporting a system for Globally Unique Identifiers based on Life Science Identifiers for biodiveristy objects such as taxon names, specimens, herbaria etc which it~~ would be ~~cool~~ to ~~integrate into any microformat~~.		The species microformats that are proposed here are a good thing. The only danger is that they re-define any of the central terms defined in the TDWG vocabularies. If they do that then they are creating another language instead of extending HTML to embrace existing semantics - which I don't think is their intent. It would be nice to have the data in web pages in a form that can be combined with the hundreds of millions of records marked up with the TDWG URIs.

	~~There~~ is a ~~meeting in~~ [http://~~tdwg2006~~.tdwg.org/ ~~St Louis, USA, October 2006~~] ~~where the way forward for the ontology will be discussed. Decisions made at the meeting will govern what is possible. It~~ is ~~difficult to take this further without concensus from that meeting.~~		If there is enough belief in the need for a Species Microformat why not propose a TDWG Applicability Statement and take it through a peer review process. The [http://www.tdwg.org/about-tdwg/process/ TDWG process] is quite simple and free (unless you count blood, sweat and tears). You would need to form a Task Group with a charter saying what you intended to do. As convener of the TAG Interest Group I would willingly host the Task Group. You could then propose a standard and have it reviewed by a range of biologists and IT people before it becomes ratified and recommended for adoption. RogerHyam 2007-11-5

	~~If it is after October 2006~~ and you ~~are interested in learning more please contact me ([[User:RogerHyam\|Roger Hyam]]~~).

	*Thanks, Roger - it's good to ~~have the involvement of such an august body, especially just before such~~ a ~~fortuitously-scheduled event~~. ~~Is there any chance (and~~ I ~~realise that this is rather late in~~ the ~~day) that this proposal~~ could ~~be on the agenda in St Louis (even if only through~~ a ~~note in the papers/ programme); or that someone from the microformat community could attend/ speak there? Or that the TDWG~~ and~~/or conference websites could link to '''http://microformats~~.~~org/wiki/species'''?~~ - ~~Andy Mabbett~~

	==Malcolm Storey==		==Malcolm Storey==

MichaelLee: /* Questions */ comments on Genus sp. and aggregate species, page size

2007-11-03T22:44:15Z

Questions: comments on Genus sp. and aggregate species, page size

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	*****[http://www.westmidlandbirdclub.com/records/lists.htm 341 species, 58Kb]. 'Nuff said? [[User:AndyMabbett\|AndyMabbett]] 11:53, 26 Sep 2006 (PDT)		*****[http://www.westmidlandbirdclub.com/records/lists.htm 341 species, 58Kb]. 'Nuff said? [[User:AndyMabbett\|AndyMabbett]] 11:53, 26 Sep 2006 (PDT)
	******Your bird list page can be [http://snipurl.com/zfmj compressed by 79%], i.e. it would go down from 58KB to 12KB by enabling output compression on your server. It would also make the page load faster and save you bandwidth. No doubt compression technologies will improve over time, as will connection speeds and server speeds, so the technical solution to reducing page size would seem to me to be preferable over the "manual compression" method, i.e. using abbreviated, less clear, less readable class names. While it is easy to improve the compression technology (or switch it on, even), it's much harder to change an established microformat standard. - [[User:CharlesRoper\| Charles Roper]]		******Your bird list page can be [http://snipurl.com/zfmj compressed by 79%], i.e. it would go down from 58KB to 12KB by enabling output compression on your server. It would also make the page load faster and save you bandwidth. No doubt compression technologies will improve over time, as will connection speeds and server speeds, so the technical solution to reducing page size would seem to me to be preferable over the "manual compression" method, i.e. using abbreviated, less clear, less readable class names. While it is easy to improve the compression technology (or switch it on, even), it's much harder to change an established microformat standard. - [[User:CharlesRoper\| Charles Roper]]
			*****Clearly page size is an issue. One way of reducing page size would be to have two versions of the page. One would be microformat marked up and the other not. It might be that the non-marked up page would be used on larger lists and as you got more refined, it would switch to marked-up pages, with the option of going with only marked-up pages or never being left to the web-user in some kind of preferences area. Styling the marked-up version into simpler HTML should be quite easy. - [[User:MichaelLee\|MichaelLee]]

	* Is "class" a potentially confusing attribute name, and what should replace it ("taxoclass", perhaps? or "classis"?)		* Is "class" a potentially confusing attribute name, and what should replace it ("taxoclass", perhaps? or "classis"?)
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	** How about the following, where we can infer an unknown species by the absence of that attribute?:		** How about the following, where we can infer an unknown species by the absence of that attribute?:
	:<pre><nowiki><span class="bin"><span class="genus">Podiceps</span></span></nowiki></pre>		:<pre><nowiki><span class="bin"><span class="genus">Podiceps</span></span></nowiki></pre>
			*** This fails to account for the fact that this is thought to be only one species of a genus. Perhaps it's better to mark the species as unknown or "sp." or even "sp. #2": [[User:MichaelLee\|MichaelLee]]
			:<pre><nowiki><span class="bin"><span class="genus">Podiceps</span><span class="species">unknown</span></span></nowiki></pre>
	** There are also species aggregates and groups to be considered Grey/Dark Dagger sp., where it is one of two species but where the genus Acronicta cannot be used as there are more than the two species in the genus - Tony Prichard		** There are also species aggregates and groups to be considered Grey/Dark Dagger sp., where it is one of two species but where the genus Acronicta cannot be used as there are more than the two species in the genus - Tony Prichard
	*** Any suggestions? Or other examples? - [[User:AndyMabbett\|AndyMabbett]]		*** Any suggestions? Or other examples? - [[User:AndyMabbett\|AndyMabbett]]
	**** This kind of aggregates are often used by birdwatchers (in Finland). How about separating the names with a slash (or some other sign)?: - [[User:MikkoBiomi\|MikkoBiomi]]		**** This kind of aggregates are often used by birdwatchers (in Finland). How about separating the names with a slash (or some other sign)?: - [[User:MikkoBiomi\|MikkoBiomi]]
	:<pre><nowiki><span class="bin">Phylloscopus trochilus/Phylloscopus collybita</span></nowiki></pre>		:<pre><nowiki><span class="bin">Phylloscopus trochilus/Phylloscopus collybita</span></nowiki></pre>
	:<pre><nowiki><span class="bin"><span class="genus">Anser</span>/<span class="genus">Branta</span></span></nowiki></pre>		:<pre><nowiki><span class="bin"><span class="genus">Anser</span>/<span class="genus">Branta</span></span></nowiki></pre>
			***** It would be clearer to come up with operators to allow a customized grouping of one's choice. Someone may want to say "I saw this or that" and one might want to say "I saw this AND that." You can use operators like / and +, but these aren't easily computer parsed. These could also be nested to come up with all sorts of groups. [[User:MichaelLee\|MichaelLee]]
			:<pre><nowiki><span class="group.or"><span class="bin">Phylloscopus trochilus</span><span>Phylloscopus collybita</span></span></nowiki></pre>
			:<pre><nowiki><span class="group.and"><span class="bin">Phylloscopus trochilus</span><span>Phylloscopus collybita</span></span></nowiki></pre>

	* Should we allow divisions of "binominal" with no parent "species", such as:		* Should we allow divisions of "binominal" with no parent "species", such as:

AndyMabbett: Other use cases

2007-08-20T11:53:31Z

Other use cases

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	:[[User:AndyMabbett\|Andy Mabbett]] 14:42, 28 Feb 2007 (PST)		:[[User:AndyMabbett\|Andy Mabbett]] 14:42, 28 Feb 2007 (PST)

			== Other use cases ==
			Please add your suggestions!

			'Species' microformats could be used to:
			*...


	==See also==		==See also==
	{{species}}		{{species}}

AndyMabbett: /* Questions */ Comment on WikiSpecies

2007-07-02T09:55:20Z

Questions: Comment on WikiSpecies

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	in which the parentheses are significant (see [http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Tree_of_Life/taxobox_usage#Authorities Wikipedia Taxobox usage] and [http://en.wikipedia.org/wiki/Author_citation_%28zoology%29 Wikipedia's article on zoological authority citations] for further examples). Should we therefore allow "authority" to be a text string, and omit a separate year field? [[User:AndyMabbett\|Andy Mabbett]] 03:17, 27 Jun 2007 (PDT)		in which the parentheses are significant (see [http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Tree_of_Life/taxobox_usage#Authorities Wikipedia Taxobox usage] and [http://en.wikipedia.org/wiki/Author_citation_%28zoology%29 Wikipedia's article on zoological authority citations] for further examples). Should we therefore allow "authority" to be a text string, and omit a separate year field? [[User:AndyMabbett\|Andy Mabbett]] 03:17, 27 Jun 2007 (PDT)

			*[http://species.wikimedia.org/w/index.php?title=Wikispecies:Village_Pump&curid=7207&diff=338726&oldid=338563 Comment on WikiSpecies, by Ucucha (19:21, 1 July 2007 UTC)]:

			:<blockquote>I definitely prefer "superregnum" over "superkingdom". Using the Latin forms of the taxon names makes the format less language-dependent and more international. It probably also reduces ambiguity somewhat (a biological "kingdom" is also called an "empire" in English).</blockquote>

	====To add====		====To add====