From tao at nceas.ucsb.edu  Wed Apr  7 19:09:00 2004
From: tao at nceas.ucsb.edu (Jing Tao)
Date: Wed, 7 Apr 2004 19:09:00 -0700 (PDT)
Subject: Eml 2 documentations
Message-ID: <Pine.LNX.4.33.0404071859150.17540-100000@hyperion.nceas.ucsb.edu>

Hi, eml gurus:

I tried to create a documentations for eml 2. I hope those docs should be 
html files with anchors to point to explain for eml element(Exactly as 
same as the eml specification in knb website).

So I check out eml with tag RELEASE_EML_2_0_0 and run "ant docs". But the 
html files don't have anchors.

If I tried to run "ant docbookhtml" and I got an error:
Processing /home/tao/project/eml/docs/eml-2.0.0/eml-docbook.xml to 
/home/tao/project/eml/docs/eml-2.0.0/index.html
    [style] Loading stylesheet 
/home/tao/project/eml/style/docbook-xsl-1.50.0/html/docbook.xsl
    [style] 
home/tao/project/eml/style/docbook-xsl-1.50.0/common/common.xsl:1385:35: 
Fatal Error! 7 >= 1 Cause: java.lang.ArrayIndexOutOfBoundsException: 7 >= 
1
    [style] : Fatal Error! Fatal error during transformation Cause: Fatal 
error during transformation
    [style] Failed to process 
/home/tao/project/eml/docs/eml-2.0.0/eml-docbook.xml

I take a look eml-docbook.xml in in docs directory. So it couldn't be 
styled.

Do you have any idea about this?

Thanks.

Jing

Jing Tao
National Center for Ecological
Analysis and Synthesis (NCEAS)
735 State St. Suite 204
Santa Barbara, CA 93101



From berkley at nceas.ucsb.edu  Thu Apr  8 09:05:13 2004
From: berkley at nceas.ucsb.edu (Chad Berkley)
Date: Thu, 8 Apr 2004 09:05:13 -0700
Subject: Eml 2 documentations
In-Reply-To: <Pine.LNX.4.33.0404071859150.17540-100000@hyperion.nceas.ucsb.edu>
References: <Pine.LNX.4.33.0404071859150.17540-100000@hyperion.nceas.ucsb.edu>
Message-ID: <84C4EBA6-8976-11D8-8BE0-000A95DA7EF8@nceas.ucsb.edu>

Hey Jing,

What version of xalan are you using?  That transform won't work with  
xalan 2.3.1 or earlier.

chad

On Apr 7, 2004, at 7:09 PM, Jing Tao wrote:

> Hi, eml gurus:
>
> I tried to create a documentations for eml 2. I hope those docs should  
> be
> html files with anchors to point to explain for eml element(Exactly as
> same as the eml specification in knb website).
>
> So I check out eml with tag RELEASE_EML_2_0_0 and run "ant docs". But  
> the
> html files don't have anchors.
>
> If I tried to run "ant docbookhtml" and I got an error:
> Processing /home/tao/project/eml/docs/eml-2.0.0/eml-docbook.xml to
> /home/tao/project/eml/docs/eml-2.0.0/index.html
>     [style] Loading stylesheet
> /home/tao/project/eml/style/docbook-xsl-1.50.0/html/docbook.xsl
>     [style]
> home/tao/project/eml/style/docbook-xsl-1.50.0/common/common.xsl:1385: 
> 35:
> Fatal Error! 7 >= 1 Cause: java.lang.ArrayIndexOutOfBoundsException: 7  
> >=
> 1
>     [style] : Fatal Error! Fatal error during transformation Cause:  
> Fatal
> error during transformation
>     [style] Failed to process
> /home/tao/project/eml/docs/eml-2.0.0/eml-docbook.xml
>
> I take a look eml-docbook.xml in in docs directory. So it couldn't be
> styled.
>
> Do you have any idea about this?
>
> Thanks.
>
> Jing
>
> Jing Tao
> National Center for Ecological
> Analysis and Synthesis (NCEAS)
> 735 State St. Suite 204
> Santa Barbara, CA 93101
>
> _______________________________________________
> eml-dev mailing list
> eml-dev at ecoinformatics.org
> http://www.ecoinformatics.org/mailman/listinfo/eml-dev



From sheldon at uga.edu  Tue Apr 13 11:27:50 2004
From: sheldon at uga.edu (Wade Sheldon)
Date: Tue, 13 Apr 2004 14:27:50 -0400
Subject: Test implementation of eml-based species lists for LTER
Message-ID: <004001c42185$072f3dc0$5449c080@GCELTERWS2>

Matt and James,

This week I have been making some changes to how we display taxonomic records on the web. As part of this process, I decided to spend a little time following through on a proposal I made during our last IMExec meeting to test eml as a format for dissemination of species lists within LTER. As a candidate document style I "trumped up" a species list data set containing the species list in taxonomicCoverage format, with appropriate title, abstract, keywords, project descriptors, etc. relevant to the purpose. I also included temporalCoverage information indicating the date the list was generated.

If you are interested in looking over my test implementation, you can generate various species lists in eml format using the web forms at: http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp

I don't currently plan to maintain versioned copies of the species list (or sub-lists) in our site data catalog, so the packageID information is basically notional; however, we could certainly do so at some point if there were interest so I left it in. I am primarily throwing this out as a candidate schema for cross-site exchange of taxonomic information. We will be working on a "eml best practices" document for LTER in the next 1-2 months, and I thought it would be good to consider recommendations for documentation of non-tabular data as well as conventional tabular data sets. Exchange/submission of bibliographic citations and personnel lists are other potential uses of eml we discussed.

Comments or recommendations would be appreciated.

--Wade Sheldon, GCE
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From jones at nceas.ucsb.edu  Tue Apr 13 12:05:02 2004
From: jones at nceas.ucsb.edu (Matt Jones)
Date: Tue, 13 Apr 2004 11:05:02 -0800
Subject: Test implementation of eml-based species lists for LTER
In-Reply-To: <004001c42185$072f3dc0$5449c080@GCELTERWS2>
References: <004001c42185$072f3dc0$5449c080@GCELTERWS2>
Message-ID: <407C39DE.7000108@nceas.ucsb.edu>

Wade,

Looks great.  You're on the leading edge yet again :)  I think using EML 
to exchange this sort of information is a great idea.  It would also be 
good to do the literature citation information this way because once 
people get used to exchanging EML it should be easy to implement.

A couple of comments about the taxonomic EML you generated:

1) When you list several taxa that share parent taxa (e.g., they are in 
the same Class), we had intended that you could nest two subtrees 
underneath the last identical rank, so that the EML representation is 
more compact.  This means, for example, that many species would be 
clustered in each genus, many genera in each family, etc up the tree. 
The only reason that I can see to separate them is if different 
taxonomicClassification systems apply (e.g., a different authority was 
used for identifications, circumscriptions, or names), and then they 
should be in different taxonomicCoverage elements.  But if they were all 
identified using the same system, then creating one tree instead of many 
I think is better.  Are there reasons you did it as you did?

2) You didn't include a taxonomicSystem element.  Although optional, I 
think this is a very important element.  It lets the user understand how 
you did identifications, and provides citations for field guides, 
taxonomic mongraphs, etc. that were used in identifying and classifying 
the organisms.  The more people do synthetic work, the more important 
this information is.  Bob Morris wrote an interesting email about the 
pitfalls of species lists to the seek-taxon list that you might find 
useful and interesting.  It was part of a larger thread where we were 
discussing species lists in general and their utility over the long 
term, especially with regard to species names versus species concepts. 
Here's the links that I think are most relevant:

Species lists:
http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000160.html

and the background for that email:
http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000159.html

Thanks again, Wade.

Matt


Wade Sheldon wrote:
> Matt and James,
>  
> This week I have been making some changes to how we display taxonomic 
> records on the web. As part of this process, I decided to spend a little 
> time following through on a proposal I made during our last IMExec 
> meeting to test eml as a format for dissemination of species lists 
> within LTER. As a candidate document style I "trumped up" a species list 
> data set containing the species list in taxonomicCoverage format, with 
> appropriate title, abstract, keywords, project descriptors, etc. 
> relevant to the purpose. I also included temporalCoverage information 
> indicating the date the list was generated.
>  
> If you are interested in looking over my test implementation, you can 
> generate various species lists in eml format using the web forms at: 
> http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp
>  
> I don't currently plan to maintain versioned copies of the species list 
> (or sub-lists) in our site data catalog, so the packageID information is 
> basically notional; however, we could certainly do so at some point if 
> there were interest so I left it in. I am primarily throwing this out as 
> a candidate schema for cross-site exchange of taxonomic information. We 
> will be working on a "eml best practices" document for LTER in the next 
> 1-2 months, and I thought it would be good to consider recommendations 
> for documentation of non-tabular data as well as conventional tabular 
> data sets. Exchange/submission of bibliographic citations and personnel 
> lists are other potential uses of eml we discussed.
>  
> Comments or recommendations would be appreciated.
>  
> --Wade Sheldon, GCE

-- 
-------------------------------------------------------------------
Matt Jones                                     jones at nceas.ucsb.edu
http://www.nceas.ucsb.edu/    Fax: 425-920-2439    Ph: 907-789-0496
National Center for Ecological Analysis and Synthesis (NCEAS)
University of California Santa Barbara
Interested in ecological informatics? http://www.ecoinformatics.org
-------------------------------------------------------------------


From rwilliams at nceas.ucsb.edu  Tue Apr 13 12:20:50 2004
From: rwilliams at nceas.ucsb.edu (Rich Williams)
Date: Tue, 13 Apr 2004 12:20:50 -0700
Subject: Test implementation of eml-based species lists for LTER
In-Reply-To: <407C39DE.7000108@nceas.ucsb.edu>
Message-ID: <PEEPIADNFBBFELFPNDCOAELJCLAA.rwilliams@nceas.ucsb.edu>

I'm curious about the specification of a two-part scientific name in the
species element (or more correctly in the taxonRankValue of the
taxonomicClassification element with taxonRankName of Species).  Is this
standard practice for EML?  I was expecting to just see the species name in
there, and not see the Genus value duplicated.  If the species always
actually contains a two-part scientific name, is there then a requirement
that the first word of the species be equal to the genus, is the genus is
present?

Rich

> -----Original Message-----
> From: eml-dev-admin at ecoinformatics.org
> [mailto:eml-dev-admin at ecoinformatics.org]On Behalf Of Matt Jones
> Sent: Tuesday, April 13, 2004 12:05 PM
> To: Wade Sheldon
> Cc: James Brunt; eml-dev at ecoinformatics.org
> Subject: Re: Test implementation of eml-based species lists for LTER
>
>
> Wade,
>
> Looks great.  You're on the leading edge yet again :)  I think using EML
> to exchange this sort of information is a great idea.  It would also be
> good to do the literature citation information this way because once
> people get used to exchanging EML it should be easy to implement.
>
> A couple of comments about the taxonomic EML you generated:
>
> 1) When you list several taxa that share parent taxa (e.g., they are in
> the same Class), we had intended that you could nest two subtrees
> underneath the last identical rank, so that the EML representation is
> more compact.  This means, for example, that many species would be
> clustered in each genus, many genera in each family, etc up the tree.
> The only reason that I can see to separate them is if different
> taxonomicClassification systems apply (e.g., a different authority was
> used for identifications, circumscriptions, or names), and then they
> should be in different taxonomicCoverage elements.  But if they were all
> identified using the same system, then creating one tree instead of many
> I think is better.  Are there reasons you did it as you did?
>
> 2) You didn't include a taxonomicSystem element.  Although optional, I
> think this is a very important element.  It lets the user understand how
> you did identifications, and provides citations for field guides,
> taxonomic mongraphs, etc. that were used in identifying and classifying
> the organisms.  The more people do synthetic work, the more important
> this information is.  Bob Morris wrote an interesting email about the
> pitfalls of species lists to the seek-taxon list that you might find
> useful and interesting.  It was part of a larger thread where we were
> discussing species lists in general and their utility over the long
> term, especially with regard to species names versus species concepts.
> Here's the links that I think are most relevant:
>
> Species lists:
> http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000160.html
>
> and the background for that email:
> http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000159.html
>
> Thanks again, Wade.
>
> Matt
>
>
> Wade Sheldon wrote:
> > Matt and James,
> >
> > This week I have been making some changes to how we display taxonomic
> > records on the web. As part of this process, I decided to spend
> a little
> > time following through on a proposal I made during our last IMExec
> > meeting to test eml as a format for dissemination of species lists
> > within LTER. As a candidate document style I "trumped up" a
> species list
> > data set containing the species list in taxonomicCoverage format, with
> > appropriate title, abstract, keywords, project descriptors, etc.
> > relevant to the purpose. I also included temporalCoverage information
> > indicating the date the list was generated.
> >
> > If you are interested in looking over my test implementation, you can
> > generate various species lists in eml format using the web forms at:
> > http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp
> >
> > I don't currently plan to maintain versioned copies of the species list
> > (or sub-lists) in our site data catalog, so the packageID
> information is
> > basically notional; however, we could certainly do so at some point if
> > there were interest so I left it in. I am primarily throwing
> this out as
> > a candidate schema for cross-site exchange of taxonomic information. We
> > will be working on a "eml best practices" document for LTER in the next
> > 1-2 months, and I thought it would be good to consider recommendations
> > for documentation of non-tabular data as well as conventional tabular
> > data sets. Exchange/submission of bibliographic citations and personnel
> > lists are other potential uses of eml we discussed.
> >
> > Comments or recommendations would be appreciated.
> >
> > --Wade Sheldon, GCE
>
> --
> -------------------------------------------------------------------
> Matt Jones                                     jones at nceas.ucsb.edu
> http://www.nceas.ucsb.edu/    Fax: 425-920-2439    Ph: 907-789-0496
> National Center for Ecological Analysis and Synthesis (NCEAS)
> University of California Santa Barbara
> Interested in ecological informatics? http://www.ecoinformatics.org
> -------------------------------------------------------------------
> _______________________________________________
> eml-dev mailing list
> eml-dev at ecoinformatics.org
> http://www.ecoinformatics.org/mailman/listinfo/eml-dev



From jones at nceas.ucsb.edu  Tue Apr 13 12:46:43 2004
From: jones at nceas.ucsb.edu (Matt Jones)
Date: Tue, 13 Apr 2004 11:46:43 -0800
Subject: Test implementation of eml-based species lists for LTER
In-Reply-To: <PEEPIADNFBBFELFPNDCOAELJCLAA.rwilliams@nceas.ucsb.edu>
References: <PEEPIADNFBBFELFPNDCOAELJCLAA.rwilliams@nceas.ucsb.edu>
Message-ID: <407C43A3.7090307@nceas.ucsb.edu>

Hi Rich,

Yeah, that is accepted practice for EML.  It derived from the same 
practice which was established for this same set of fields for the NBII 
Biological Data Profile (BDP).  Feedback for the said that the species 
part of a binomial epithet is *never* written without the genus part of 
the binomial, and the subspecies part is *never* written without the 
species and genus part.  A number of established taxonomists objected 
strongly to having a field for species which did not include the Genus, 
even though the Genus was above it in a field. Soo...the Biological Data 
WOrking Group agreed to modify the BDP to require that the Species rank 
include the whole binomial, and that Subspecies rank includes the whole 
trinomial.

EML strives to be compatible with the BDP, so we simply adopted there 
conventions, although not without substantial debate over about a year. 
  Nevertheless, I think it is a poor design, but I kind of feel stuck 
with it.  Maybe if everyone using EML were to agree that it could or 
should be just a monomial, then we could change it in a future version 
of EML (we can of course generate the needed binomials and trinomials 
from the individual components as needed to generate BDP metadata. 
Comments appreciated.

Matt

Rich Williams wrote:
> I'm curious about the specification of a two-part scientific name in the
> species element (or more correctly in the taxonRankValue of the
> taxonomicClassification element with taxonRankName of Species).  Is this
> standard practice for EML?  I was expecting to just see the species name in
> there, and not see the Genus value duplicated.  If the species always
> actually contains a two-part scientific name, is there then a requirement
> that the first word of the species be equal to the genus, is the genus is
> present?
> 
> Rich
> 
> 
>>-----Original Message-----
>>From: eml-dev-admin at ecoinformatics.org
>>[mailto:eml-dev-admin at ecoinformatics.org]On Behalf Of Matt Jones
>>Sent: Tuesday, April 13, 2004 12:05 PM
>>To: Wade Sheldon
>>Cc: James Brunt; eml-dev at ecoinformatics.org
>>Subject: Re: Test implementation of eml-based species lists for LTER
>>
>>
>>Wade,
>>
>>Looks great.  You're on the leading edge yet again :)  I think using EML
>>to exchange this sort of information is a great idea.  It would also be
>>good to do the literature citation information this way because once
>>people get used to exchanging EML it should be easy to implement.
>>
>>A couple of comments about the taxonomic EML you generated:
>>
>>1) When you list several taxa that share parent taxa (e.g., they are in
>>the same Class), we had intended that you could nest two subtrees
>>underneath the last identical rank, so that the EML representation is
>>more compact.  This means, for example, that many species would be
>>clustered in each genus, many genera in each family, etc up the tree.
>>The only reason that I can see to separate them is if different
>>taxonomicClassification systems apply (e.g., a different authority was
>>used for identifications, circumscriptions, or names), and then they
>>should be in different taxonomicCoverage elements.  But if they were all
>>identified using the same system, then creating one tree instead of many
>>I think is better.  Are there reasons you did it as you did?
>>
>>2) You didn't include a taxonomicSystem element.  Although optional, I
>>think this is a very important element.  It lets the user understand how
>>you did identifications, and provides citations for field guides,
>>taxonomic mongraphs, etc. that were used in identifying and classifying
>>the organisms.  The more people do synthetic work, the more important
>>this information is.  Bob Morris wrote an interesting email about the
>>pitfalls of species lists to the seek-taxon list that you might find
>>useful and interesting.  It was part of a larger thread where we were
>>discussing species lists in general and their utility over the long
>>term, especially with regard to species names versus species concepts.
>>Here's the links that I think are most relevant:
>>
>>Species lists:
>>http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000160.html
>>
>>and the background for that email:
>>http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000159.html
>>
>>Thanks again, Wade.
>>
>>Matt
>>
>>
>>Wade Sheldon wrote:
>>
>>>Matt and James,
>>>
>>>This week I have been making some changes to how we display taxonomic
>>>records on the web. As part of this process, I decided to spend
>>
>>a little
>>
>>>time following through on a proposal I made during our last IMExec
>>>meeting to test eml as a format for dissemination of species lists
>>>within LTER. As a candidate document style I "trumped up" a
>>
>>species list
>>
>>>data set containing the species list in taxonomicCoverage format, with
>>>appropriate title, abstract, keywords, project descriptors, etc.
>>>relevant to the purpose. I also included temporalCoverage information
>>>indicating the date the list was generated.
>>>
>>>If you are interested in looking over my test implementation, you can
>>>generate various species lists in eml format using the web forms at:
>>>http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp
>>>
>>>I don't currently plan to maintain versioned copies of the species list
>>>(or sub-lists) in our site data catalog, so the packageID
>>
>>information is
>>
>>>basically notional; however, we could certainly do so at some point if
>>>there were interest so I left it in. I am primarily throwing
>>
>>this out as
>>
>>>a candidate schema for cross-site exchange of taxonomic information. We
>>>will be working on a "eml best practices" document for LTER in the next
>>>1-2 months, and I thought it would be good to consider recommendations
>>>for documentation of non-tabular data as well as conventional tabular
>>>data sets. Exchange/submission of bibliographic citations and personnel
>>>lists are other potential uses of eml we discussed.
>>>
>>>Comments or recommendations would be appreciated.
>>>
>>>--Wade Sheldon, GCE
>>
>>--
>>-------------------------------------------------------------------
>>Matt Jones                                     jones at nceas.ucsb.edu
>>http://www.nceas.ucsb.edu/    Fax: 425-920-2439    Ph: 907-789-0496
>>National Center for Ecological Analysis and Synthesis (NCEAS)
>>University of California Santa Barbara
>>Interested in ecological informatics? http://www.ecoinformatics.org
>>-------------------------------------------------------------------
>>_______________________________________________
>>eml-dev mailing list
>>eml-dev at ecoinformatics.org
>>http://www.ecoinformatics.org/mailman/listinfo/eml-dev

-- 
-------------------------------------------------------------------
Matt Jones                                     jones at nceas.ucsb.edu
http://www.nceas.ucsb.edu/    Fax: 425-920-2439    Ph: 907-789-0496
National Center for Ecological Analysis and Synthesis (NCEAS)
University of California Santa Barbara
Interested in ecological informatics? http://www.ecoinformatics.org
-------------------------------------------------------------------


From sheldon at uga.edu  Tue Apr 13 12:48:33 2004
From: sheldon at uga.edu (Wade Sheldon)
Date: Tue, 13 Apr 2004 15:48:33 -0400
Subject: Test implementation of eml-based species lists for LTER
References: <004001c42185$072f3dc0$5449c080@GCELTERWS2> <407C39DE.7000108@nceas.ucsb.edu>
Message-ID: <002001c42190$4de97810$5449c080@GCELTERWS2>

Matt,

Thanks. Regarding your points:

> 1) When you list several taxa that share parent taxa (e.g., they are in
> the same Class), we had intended that you could nest two subtrees
> underneath the last identical rank, so that the EML representation is
> more compact.  This means, for example, that many species would be
> clustered in each genus, many genera in each family, etc up the tree.
> The only reason that I can see to separate them is if different
> taxonomicClassification systems apply (e.g., a different authority was
> used for identifications, circumscriptions, or names), and then they
> should be in different taxonomicCoverage elements.  But if they were all
> identified using the same system, then creating one tree instead of many
> I think is better.  Are there reasons you did it as you did?

This is an artifact of how I am pre-generating xml fragments in SQL views
for populating taxonomicCoverage for ecological data sets that contain
species references (ie. one complete taxonomicClassification fragment for
each species record). I can certainly use a different approach and group
within common ranks for the purpose of list generation if that would be
preferable. The queries I use to generate csv text files return granular
taxonomic rank/value pairs, so it would be easy to program the roll-ups
within taxa using a stack approach. I'll take a stab at that and offer it as
an alternative schema for consideration.

>
> 2) You didn't include a taxonomicSystem element.  Although optional, I
> think this is a very important element.  It lets the user understand how
> you did identifications, and provides citations for field guides,
> taxonomic mongraphs, etc. that were used in identifying and classifying
> the organisms.  The more people do synthetic work, the more important
> this information is.  Bob Morris wrote an interesting email about the
> pitfalls of species lists to the seek-taxon list that you might find
> useful and interesting.  It was part of a larger thread where we were
> discussing species lists in general and their utility over the long
> term, especially with regard to species names versus species concepts.
> Here's the links that I think are most relevant:

I will add this information, along with individualName contact info for the
GCE scientists who contributed the entries, if this list proves useful.

> Species lists:
> http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000160.html
>
> and the background for that email:
> http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000159.html

Thanks for the links. I'll take a look.

--Wade



From sheldon at uga.edu  Wed Apr 14 15:30:36 2004
From: sheldon at uga.edu (Wade Sheldon)
Date: Wed, 14 Apr 2004 18:30:36 -0400
Subject: Test implementation of eml-based species lists for LTER
References: <004001c42185$072f3dc0$5449c080@GCELTERWS2> <407C39DE.7000108@nceas.ucsb.edu>
Message-ID: <008501c42270$1bcbf750$5449c080@GCELTERWS2>

Matt,

It was a lot harder than I anticipated, but I did manage to write an
algorithm to generate phylogenetic trees in eml based on taxonomic rank
name/value pairs. It was a headache sorting out the element nesting while
dealing with varying taxa depth and nulls (i.e. varying levels of taxonomic
completeness for species records in the database), but it works.

I added an "EML (tree)" option and relabeled the original implementation as
"EML (list)", so both are available unless we eventually conclude that only
one is useful. Here again is the url:
http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp

I made the decision to group records with less detailed higher level taxa
below records with more detail (i.e. last node on the highest common
branch), but that was somewhat arbitrary. For example, we have 7 bivalve
mollusc records, and 6 contain entries for kingdom, phylum, class, order,
genus, species but one contains entries for kingdom, phylum, class,
superfamily, family, genus, species. In my eml doc these would be arranged
in the tree as:

kingdom
    phylum
        class
            orderA
                genus1
                    species1
                genus2
                    species2
                genus3
                    species3
            orderB
                genus4
                    species4
                genus5
                    species5
                genus6
                    species6
            superfamily
                family
                    genus7
                        species7
...

Otherwise in the case above the green mussel record without an order entry
would appear as the first branch below class, which seemed odd to me (i.e.
having superfamily branches above order branches in the tree).

Anyway, thanks for the feedback.

--Wade Sheldon, GCE-LTER


----- Original Message ----- 
From: "Matt Jones" <jones at nceas.ucsb.edu>
To: "Wade Sheldon" <sheldon at uga.edu>
Cc: "James Brunt" <jbrunt at lternet.edu>; <eml-dev at ecoinformatics.org>
Sent: Tuesday, April 13, 2004 3:05 PM
Subject: Re: Test implementation of eml-based species lists for LTER


> Wade,
>
> Looks great.  You're on the leading edge yet again :)  I think using EML
> to exchange this sort of information is a great idea.  It would also be
> good to do the literature citation information this way because once
> people get used to exchanging EML it should be easy to implement.
>
> A couple of comments about the taxonomic EML you generated:
>
> 1) When you list several taxa that share parent taxa (e.g., they are in
> the same Class), we had intended that you could nest two subtrees
> underneath the last identical rank, so that the EML representation is
> more compact.  This means, for example, that many species would be
> clustered in each genus, many genera in each family, etc up the tree.
> The only reason that I can see to separate them is if different
> taxonomicClassification systems apply (e.g., a different authority was
> used for identifications, circumscriptions, or names), and then they
> should be in different taxonomicCoverage elements.  But if they were all
> identified using the same system, then creating one tree instead of many
> I think is better.  Are there reasons you did it as you did?
>
> 2) You didn't include a taxonomicSystem element.  Although optional, I
> think this is a very important element.  It lets the user understand how
> you did identifications, and provides citations for field guides,
> taxonomic mongraphs, etc. that were used in identifying and classifying
> the organisms.  The more people do synthetic work, the more important
> this information is.  Bob Morris wrote an interesting email about the
> pitfalls of species lists to the seek-taxon list that you might find
> useful and interesting.  It was part of a larger thread where we were
> discussing species lists in general and their utility over the long
> term, especially with regard to species names versus species concepts.
> Here's the links that I think are most relevant:
>
> Species lists:
> http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000160.html
>
> and the background for that email:
> http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000159.html
>
> Thanks again, Wade.
>
> Matt
>
>
> Wade Sheldon wrote:
> > Matt and James,
> >
> > This week I have been making some changes to how we display taxonomic
> > records on the web. As part of this process, I decided to spend a little
> > time following through on a proposal I made during our last IMExec
> > meeting to test eml as a format for dissemination of species lists
> > within LTER. As a candidate document style I "trumped up" a species list
> > data set containing the species list in taxonomicCoverage format, with
> > appropriate title, abstract, keywords, project descriptors, etc.
> > relevant to the purpose. I also included temporalCoverage information
> > indicating the date the list was generated.
> >
> > If you are interested in looking over my test implementation, you can
> > generate various species lists in eml format using the web forms at:
> > http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp
> >
> > I don't currently plan to maintain versioned copies of the species list
> > (or sub-lists) in our site data catalog, so the packageID information is
> > basically notional; however, we could certainly do so at some point if
> > there were interest so I left it in. I am primarily throwing this out as
> > a candidate schema for cross-site exchange of taxonomic information. We
> > will be working on a "eml best practices" document for LTER in the next
> > 1-2 months, and I thought it would be good to consider recommendations
> > for documentation of non-tabular data as well as conventional tabular
> > data sets. Exchange/submission of bibliographic citations and personnel
> > lists are other potential uses of eml we discussed.
> >
> > Comments or recommendations would be appreciated.
> >
> > --Wade Sheldon, GCE
>
> -- 
> -------------------------------------------------------------------
> Matt Jones                                     jones at nceas.ucsb.edu
> http://www.nceas.ucsb.edu/    Fax: 425-920-2439    Ph: 907-789-0496
> National Center for Ecological Analysis and Synthesis (NCEAS)
> University of California Santa Barbara
> Interested in ecological informatics? http://www.ecoinformatics.org
> -------------------------------------------------------------------
>



From sheldon at uga.edu  Thu Apr 15 07:01:00 2004
From: sheldon at uga.edu (Wade Sheldon)
Date: Thu, 15 Apr 2004 10:01:00 -0400
Subject: Test implementation of eml-based species lists for LTER
References: <004001c42185$072f3dc0$5449c080@GCELTERWS2> <407C39DE.7000108@nceas.ucsb.edu> <008501c42270$1bcbf750$5449c080@GCELTERWS2>
Message-ID: <004701c422f2$15345e00$5449c080@GCELTERWS2>

Matt,

This morning I thought of a good reason to keep both eml species list
implements (i.e. complete hierarchy per record + compact tree form). For the
purpose of species list exchange within LTER it would be somewhat easier to
program against the complete record schema for populating a master list or
centralized database; otherwise, any parser would have to walk each tree and
regenerate all the common ranks that were removed before doing anything
else. That isn't terribly difficult (I do that all the time with RDP trees
in my bioinformatics work), but it's another significant step.

I also think that the first model would be easier for sites struggling with
xml generation to accomplish. Nesting taxonomicClassification tags is enough
of a programming headache without throwing tree generation into the mix. I
agree that the tree form is superior for display of taxonomic coverage,
though, and I will implement that for our data set eml as well now that I
have developed a working algorithm and corresponding SQL views.

--Wade


----- Original Message ----- 
From: "Wade Sheldon" <sheldon at uga.edu>
To: "Matt Jones" <jones at nceas.ucsb.edu>
Cc: "James Brunt" <jbrunt at lternet.edu>; <eml-dev at ecoinformatics.org>
Sent: Wednesday, April 14, 2004 6:30 PM
Subject: Re: Test implementation of eml-based species lists for LTER


> Matt,
>
> It was a lot harder than I anticipated, but I did manage to write an
> algorithm to generate phylogenetic trees in eml based on taxonomic rank
> name/value pairs. It was a headache sorting out the element nesting while
> dealing with varying taxa depth and nulls (i.e. varying levels of
taxonomic
> completeness for species records in the database), but it works.
>
> I added an "EML (tree)" option and relabeled the original implementation
as
> "EML (list)", so both are available unless we eventually conclude that
only
> one is useful. Here again is the url:
> http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp
>
> I made the decision to group records with less detailed higher level taxa
> below records with more detail (i.e. last node on the highest common
> branch), but that was somewhat arbitrary. For example, we have 7 bivalve
> mollusc records, and 6 contain entries for kingdom, phylum, class, order,
> genus, species but one contains entries for kingdom, phylum, class,
> superfamily, family, genus, species. In my eml doc these would be arranged
> in the tree as:
>
> kingdom
>     phylum
>         class
>             orderA
>                 genus1
>                     species1
>                 genus2
>                     species2
>                 genus3
>                     species3
>             orderB
>                 genus4
>                     species4
>                 genus5
>                     species5
>                 genus6
>                     species6
>             superfamily
>                 family
>                     genus7
>                         species7
> ..
>
> Otherwise in the case above the green mussel record without an order entry
> would appear as the first branch below class, which seemed odd to me (i.e.
> having superfamily branches above order branches in the tree).
>
> Anyway, thanks for the feedback.
>
> --Wade Sheldon, GCE-LTER
>
>
> ----- Original Message ----- 
> From: "Matt Jones" <jones at nceas.ucsb.edu>
> To: "Wade Sheldon" <sheldon at uga.edu>
> Cc: "James Brunt" <jbrunt at lternet.edu>; <eml-dev at ecoinformatics.org>
> Sent: Tuesday, April 13, 2004 3:05 PM
> Subject: Re: Test implementation of eml-based species lists for LTER
>
>
> > Wade,
> >
> > Looks great.  You're on the leading edge yet again :)  I think using EML
> > to exchange this sort of information is a great idea.  It would also be
> > good to do the literature citation information this way because once
> > people get used to exchanging EML it should be easy to implement.
> >
> > A couple of comments about the taxonomic EML you generated:
> >
> > 1) When you list several taxa that share parent taxa (e.g., they are in
> > the same Class), we had intended that you could nest two subtrees
> > underneath the last identical rank, so that the EML representation is
> > more compact.  This means, for example, that many species would be
> > clustered in each genus, many genera in each family, etc up the tree.
> > The only reason that I can see to separate them is if different
> > taxonomicClassification systems apply (e.g., a different authority was
> > used for identifications, circumscriptions, or names), and then they
> > should be in different taxonomicCoverage elements.  But if they were all
> > identified using the same system, then creating one tree instead of many
> > I think is better.  Are there reasons you did it as you did?
> >
> > 2) You didn't include a taxonomicSystem element.  Although optional, I
> > think this is a very important element.  It lets the user understand how
> > you did identifications, and provides citations for field guides,
> > taxonomic mongraphs, etc. that were used in identifying and classifying
> > the organisms.  The more people do synthetic work, the more important
> > this information is.  Bob Morris wrote an interesting email about the
> > pitfalls of species lists to the seek-taxon list that you might find
> > useful and interesting.  It was part of a larger thread where we were
> > discussing species lists in general and their utility over the long
> > term, especially with regard to species names versus species concepts.
> > Here's the links that I think are most relevant:
> >
> > Species lists:
> >
http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000160.html
> >
> > and the background for that email:
> >
http://www.ecoinformatics.org/pipermail/seek-taxon/2004-March/000159.html
> >
> > Thanks again, Wade.
> >
> > Matt
> >
> >
> > Wade Sheldon wrote:
> > > Matt and James,
> > >
> > > This week I have been making some changes to how we display taxonomic
> > > records on the web. As part of this process, I decided to spend a
little
> > > time following through on a proposal I made during our last IMExec
> > > meeting to test eml as a format for dissemination of species lists
> > > within LTER. As a candidate document style I "trumped up" a species
list
> > > data set containing the species list in taxonomicCoverage format, with
> > > appropriate title, abstract, keywords, project descriptors, etc.
> > > relevant to the purpose. I also included temporalCoverage information
> > > indicating the date the list was generated.
> > >
> > > If you are interested in looking over my test implementation, you can
> > > generate various species lists in eml format using the web forms at:
> > > http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp
> > >
> > > I don't currently plan to maintain versioned copies of the species
list
> > > (or sub-lists) in our site data catalog, so the packageID information
is
> > > basically notional; however, we could certainly do so at some point if
> > > there were interest so I left it in. I am primarily throwing this out
as
> > > a candidate schema for cross-site exchange of taxonomic information.
We
> > > will be working on a "eml best practices" document for LTER in the
next
> > > 1-2 months, and I thought it would be good to consider recommendations
> > > for documentation of non-tabular data as well as conventional tabular
> > > data sets. Exchange/submission of bibliographic citations and
personnel
> > > lists are other potential uses of eml we discussed.
> > >
> > > Comments or recommendations would be appreciated.
> > >
> > > --Wade Sheldon, GCE
> >
> > -- 
> > -------------------------------------------------------------------
> > Matt Jones                                     jones at nceas.ucsb.edu
> > http://www.nceas.ucsb.edu/    Fax: 425-920-2439    Ph: 907-789-0496
> > National Center for Ecological Analysis and Synthesis (NCEAS)
> > University of California Santa Barbara
> > Interested in ecological informatics? http://www.ecoinformatics.org
> > -------------------------------------------------------------------
> >
>
> _______________________________________________
> eml-dev mailing list
> eml-dev at ecoinformatics.org
> http://www.ecoinformatics.org/mailman/listinfo/eml-dev
>



From bugzilla-daemon at ecoinformatics.org  Fri Apr 30 15:09:21 2004
From: bugzilla-daemon at ecoinformatics.org (bugzilla-daemon@ecoinformatics.org)
Date: Fri, 30 Apr 2004 15:09:21 -0700 (PDT)
Subject: [Bug 1132]  - fix access control rule ambiguities
Message-ID: <20040430220921.48B44B74D2@ecoinfo.nceas.ucsb.edu>

http://bugzilla.ecoinformatics.org/show_bug.cgi?id=1132

sgarg at nceas.ucsb.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
OtherBugsDependingO|                            |968
              nThis|                            |


