From jones at nceas.ucsb.edu  Mon Apr  4 11:47:04 2005
From: jones at nceas.ucsb.edu (Matt Jones)
Date: Mon, 04 Apr 2005 10:47:04 -0800
Subject: [eml-dev] [Fwd: Re: EML units  - pH]
Message-ID: <42518BA8.4060608@nceas.ucsb.edu>


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From higgins at nceas.ucsb.edu  Mon Apr  4 12:06:29 2005
From: higgins at nceas.ucsb.edu (Dan Higgins)
Date: Mon, 04 Apr 2005 12:06:29 -0700
Subject: [eml-dev] [Fwd: Re: EML units  - pH]
In-Reply-To: <42518BA8.4060608@nceas.ucsb.edu>
References: <42518BA8.4060608@nceas.ucsb.edu>
Message-ID: <42519035.7050803@nceas.ucsb.edu>

Hi All,
    As I learned it, a mole (of anything) is not a mass (grams). It is a 
_count _in units of Avagado's number (6.023x10^23) Or, as defined by NIST

The mole is the amount of substance of a system which contains as many 
elementary entities as there are atoms in 0.012 kilogram of carbon 12

It thus really has no units.

Dan

----

Matt Jones wrote:

>
> ------------------------------------------------------------------------
>
> Subject:
> Re: EML units - pH
> From:
> Matt Jones <jones at nceas.ucsb.edu>
> Date:
> Mon, 04 Apr 2005 10:46:18 -0800
> To:
> David Balsiger <dbalsiger at wisc.edu>
>
> To:
> David Balsiger <dbalsiger at wisc.edu>
> CC:
> servilla at lternet.edu, sheldon at uga.edu, bjbenson at wisc.edu, 
> pmkapadia at wisc.edu
>
>
> This is a tricky one that we discussed a lot in the eml group but were 
> ultimately stymied.  Here's the basics as I recall it:
>
> pH = -log(moles H/liter)
>
> moles H =~ grams because the molecular weight of H is 1
>
> thus,
>
> pH =~ -log(grams H/liter)
>
> For example, for a solution with hydrogen ion concentration of 10^?4, 
> or 0.0001, moles per liter, the pH is 4.
>
> The problem we run into is how to deal with the -log, which doesn't 
> really change the units.  STMML doesn't really deal with 
> transformations like this, so we weren't really sure how to either.  
> The unit seems like it should be -log(moles/l) [or for hydrogen maybe 
> -log(grams/liter)], but we didn't really know what to make of it 
> because STMML has no way to express functions such as logarithms as 
> far as we could tell.  Its possible that transformaitons like this 
> make the value dimensionless, but I'm not sure.  This problem extends 
> beyond pH to other similar transformations such as sin, cos, etc., but 
> pH seems a very common case. STMML probably would need to be extended 
> with a general purpose expression language that supports common 
> transformation functions to really define pH.  Suggestions are welcome 
> on how to handle this in the EML units description.
>
> Matt
>
> David Balsiger wrote:
>
>> Matt, Mark, Wade,
>>
>> Surely someone has determined the correct unit and unit/type 
>> descriptions for standard pH measurements. Can you save us some time 
>> and effort in this matter?
>>
>> Thanks
>> Dave
>>
>>
>> Dave Balsiger   Center for Limnology  265-7944
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Eml-dev mailing list
>Eml-dev at ecoinformatics.org
>http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/eml-dev
>  
>


-- 
*******************************************************************
Dan Higgins                                  higgins at nceas.ucsb.edu
http://www.nceas.ucsb.edu/    Ph: 805-893-5127
National Center for Ecological Analysis and Synthesis (NCEAS) 
Marine Science Building - Room 3405
Santa Barbara, CA 93195
*******************************************************************


From jones at nceas.ucsb.edu  Mon Apr  4 12:27:23 2005
From: jones at nceas.ucsb.edu (Matt Jones)
Date: Mon, 04 Apr 2005 11:27:23 -0800
Subject: [eml-dev] [Fwd: Re: EML units  - pH]
In-Reply-To: <42519035.7050803@nceas.ucsb.edu>
References: <42518BA8.4060608@nceas.ucsb.edu> <42519035.7050803@nceas.ucsb.edu>
Message-ID: <4251951B.3010707@nceas.ucsb.edu>

Uh, true, sort of.  In addition, I think the mass of a mole of particles 
can be calculated as the # moles x molecular weight, which for hydrogen 
is 1, so one mole of hydrogen = 1 gram of hydrogen.  So there is a 
direct relationship between moles and mass that varies as a function of 
molecular weight.  So a mole is a count that is directly porportional to 
mass.

In addition, "mole" is the fundamental SI unit for the NIST fundamental 
dimension "amount", so mole itself can be used in derived unit types. 
So the only problem I really encounter in the definition of the units 
for pH is how to deal with the log(), not the molar concentration issue.

Matt

Dan Higgins wrote:
> Hi All,
>    As I learned it, a mole (of anything) is not a mass (grams). It is a 
> _count _in units of Avagado's number (6.023x10^23) Or, as defined by NIST
> 
> The mole is the amount of substance of a system which contains as many 
> elementary entities as there are atoms in 0.012 kilogram of carbon 12
> 
> It thus really has no units.
> 
> Dan
> 
> ----
> 
> Matt Jones wrote:
> 
>>
>> ------------------------------------------------------------------------
>>
>> Subject:
>> Re: EML units - pH
>> From:
>> Matt Jones <jones at nceas.ucsb.edu>
>> Date:
>> Mon, 04 Apr 2005 10:46:18 -0800
>> To:
>> David Balsiger <dbalsiger at wisc.edu>
>>
>> To:
>> David Balsiger <dbalsiger at wisc.edu>
>> CC:
>> servilla at lternet.edu, sheldon at uga.edu, bjbenson at wisc.edu, 
>> pmkapadia at wisc.edu
>>
>>
>> This is a tricky one that we discussed a lot in the eml group but were 
>> ultimately stymied.  Here's the basics as I recall it:
>>
>> pH = -log(moles H/liter)
>>
>> moles H =~ grams because the molecular weight of H is 1
>>
>> thus,
>>
>> pH =~ -log(grams H/liter)
>>
>> For example, for a solution with hydrogen ion concentration of 10^?4, 
>> or 0.0001, moles per liter, the pH is 4.
>>
>> The problem we run into is how to deal with the -log, which doesn't 
>> really change the units.  STMML doesn't really deal with 
>> transformations like this, so we weren't really sure how to either.  
>> The unit seems like it should be -log(moles/l) [or for hydrogen maybe 
>> -log(grams/liter)], but we didn't really know what to make of it 
>> because STMML has no way to express functions such as logarithms as 
>> far as we could tell.  Its possible that transformaitons like this 
>> make the value dimensionless, but I'm not sure.  This problem extends 
>> beyond pH to other similar transformations such as sin, cos, etc., but 
>> pH seems a very common case. STMML probably would need to be extended 
>> with a general purpose expression language that supports common 
>> transformation functions to really define pH.  Suggestions are welcome 
>> on how to handle this in the EML units description.
>>
>> Matt
>>
>> David Balsiger wrote:
>>
>>> Matt, Mark, Wade,
>>>
>>> Surely someone has determined the correct unit and unit/type 
>>> descriptions for standard pH measurements. Can you save us some time 
>>> and effort in this matter?
>>>
>>> Thanks
>>> Dave
>>>
>>>
>>> Dave Balsiger   Center for Limnology  265-7944
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Eml-dev mailing list
>> Eml-dev at ecoinformatics.org
>> http://mercury.nceas.ucsb.edu/ecoinformatics/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 isangil at lternet.edu  Mon Apr  4 12:28:42 2005
From: isangil at lternet.edu (Inigo San Gil)
Date: Mon, 04 Apr 2005 13:28:42 -0600
Subject: [eml-dev] [Fwd: Re: EML units  - pH]
In-Reply-To: <42519035.7050803@nceas.ucsb.edu>
References: <42518BA8.4060608@nceas.ucsb.edu> <42519035.7050803@nceas.ucsb.edu>
Message-ID: <4251956A.2090109@lternet.edu>


Agree. A mol(e) is a number --dimensionless-- 6.023 * 10^23. I.e; one 
mole of potatoes.  A mole of whatever is that outrageously big number of 
whatever.. Other thing is how much weights a mole of oxygen. (Hence the 
reference for "the molecular weight" of elements)

    * An Avogadro's number of standard soft drink cans would cover the
      surface of the earth to a depth of over 200 miles.
    * If you had Avogadro's number of unpopped popcorn kernels, and
      spread them across the United States of America, the country would
      be covered in popcorn to a depth of over 9 miles.
    * If we were able to count atoms at the rate of 10 million per
      second, it would take about 2 billion years to count the atoms in
      one mole.

The man's last name was Avogadro, not that it matters, but to give him 
the credit he did not receive while alive. The scientific community 
ignore his claims in favor to those of Dalton. Dalton was the man in 
vogue during those years, (main claim: the atom is an undivisible 
entity) and Avogadro was.. just plain ugly. His explanations of Gay 
Lussac findings were just ignored. Some websites had different theories 
about why this happened 
http://www.chemheritage.org/EducationalServices/chemach/ppt/aa.html

cheers, inigo




Dan Higgins wrote:

>Hi All,
>    As I learned it, a mole (of anything) is not a mass (grams). It is a 
>_count _in units of Avagado's number (6.023x10^23) Or, as defined by NIST
>
>The mole is the amount of substance of a system which contains as many 
>elementary entities as there are atoms in 0.012 kilogram of carbon 12
>
>It thus really has no units.
>
>Dan
>
>----
>
>Matt Jones wrote:
>
>  
>
>>------------------------------------------------------------------------
>>
>>Subject:
>>Re: EML units - pH
>>From:
>>Matt Jones <jones at nceas.ucsb.edu>
>>Date:
>>Mon, 04 Apr 2005 10:46:18 -0800
>>To:
>>David Balsiger <dbalsiger at wisc.edu>
>>
>>To:
>>David Balsiger <dbalsiger at wisc.edu>
>>CC:
>>servilla at lternet.edu, sheldon at uga.edu, bjbenson at wisc.edu, 
>>pmkapadia at wisc.edu
>>
>>
>>This is a tricky one that we discussed a lot in the eml group but were 
>>ultimately stymied.  Here's the basics as I recall it:
>>
>>pH = -log(moles H/liter)
>>
>>moles H =~ grams because the molecular weight of H is 1
>>
>>thus,
>>
>>pH =~ -log(grams H/liter)
>>
>>For example, for a solution with hydrogen ion concentration of 10^?4, 
>>or 0.0001, moles per liter, the pH is 4.
>>
>>The problem we run into is how to deal with the -log, which doesn't 
>>really change the units.  STMML doesn't really deal with 
>>transformations like this, so we weren't really sure how to either.  
>>The unit seems like it should be -log(moles/l) [or for hydrogen maybe 
>>-log(grams/liter)], but we didn't really know what to make of it 
>>because STMML has no way to express functions such as logarithms as 
>>far as we could tell.  Its possible that transformaitons like this 
>>make the value dimensionless, but I'm not sure.  This problem extends 
>>beyond pH to other similar transformations such as sin, cos, etc., but 
>>pH seems a very common case. STMML probably would need to be extended 
>>with a general purpose expression language that supports common 
>>transformation functions to really define pH.  Suggestions are welcome 
>>on how to handle this in the EML units description.
>>
>>Matt
>>
>>David Balsiger wrote:
>>
>>    
>>
>>>Matt, Mark, Wade,
>>>
>>>Surely someone has determined the correct unit and unit/type 
>>>descriptions for standard pH measurements. Can you save us some time 
>>>and effort in this matter?
>>>
>>>Thanks
>>>Dave
>>>
>>>
>>>Dave Balsiger   Center for Limnology  265-7944
>>>      
>>>
>>------------------------------------------------------------------------
>>
>>_______________________________________________
>>Eml-dev mailing list
>>Eml-dev at ecoinformatics.org
>>http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/eml-dev
>> 
>>
>>    
>>
>
>
>  
>


From xiaoping.y.wang at noaa.gov  Tue Apr  5 14:32:55 2005
From: xiaoping.y.wang at noaa.gov (Xiaoping Wang)
Date: Tue, 05 Apr 2005 14:32:55 -0700
Subject: [eml-dev] precision
In-Reply-To: <4251951B.3010707@nceas.ucsb.edu>
References: <42518BA8.4060608@nceas.ucsb.edu> <42519035.7050803@nceas.ucsb.edu>
	<4251951B.3010707@nceas.ucsb.edu>
Message-ID: <42530407.3020400@noaa.gov>

Based on EML 2.0.1 specification, the precision element for ratio is 
optional.  However, I always get the following error message if the 
value for the precision is not provided:

cvc-complex-type.2.4.a: Invalid content starting with element 
'numericDomain'. The content must match 
'((("":unit),("":precision){1-UNBOUNDED}),("":numericDomain))'.

Is this a bug or do I misunderstand the schema?  Please help!

We have many data that do not have a precision defined. 

Thanks!

Xiaoping Wang

PMEL / NOAA



From jones at nceas.ucsb.edu  Tue Apr  5 15:47:33 2005
From: jones at nceas.ucsb.edu (Matt Jones)
Date: Tue, 05 Apr 2005 14:47:33 -0800
Subject: [eml-dev] precision
In-Reply-To: <42530407.3020400@noaa.gov>
References: <42518BA8.4060608@nceas.ucsb.edu> <42519035.7050803@nceas.ucsb.edu>
	<4251951B.3010707@nceas.ucsb.edu> <42530407.3020400@noaa.gov>
Message-ID: <42531585.6030508@nceas.ucsb.edu>

precision was required in EML 2.0.0 -- are you sure your document says 
it is an EML 2.0.1 document?  Morpho currently generates EML 2.0.0 
documents, so unless you explicitly change it you would see that error. 
  You can find out what the document type is by looking at the EML 
namesapce at the top of the XML document.

Matt

Xiaoping Wang wrote:
> Based on EML 2.0.1 specification, the precision element for ratio is 
> optional.  However, I always get the following error message if the 
> value for the precision is not provided:
> 
> cvc-complex-type.2.4.a: Invalid content starting with element 
> 'numericDomain'. The content must match 
> '((("":unit),("":precision){1-UNBOUNDED}),("":numericDomain))'.
> 
> Is this a bug or do I misunderstand the schema?  Please help!
> 
> We have many data that do not have a precision defined.
> Thanks!
> 
> Xiaoping Wang
> 
> PMEL / NOAA
> 

-- 
-------------------------------------------------------------------
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 12 16:55:51 2005
From: sheldon at uga.edu (Wade Sheldon)
Date: Tue, 12 Apr 2005 19:55:51 -0400
Subject: [eml-dev] Recommendations for reporting file access errors to
	software agents
In-Reply-To: <42545DBE.4080104@nceas.ucsb.edu>
References: <E1DJI8I-0004DK-00@lternet.lternet.edu>
	<42545DBE.4080104@nceas.ucsb.edu>
Message-ID: <425C6007.4020802@uga.edu>

Matt and all,

What type of error message (content and formatting) do you think should be
returned to a software agent that tries to retrieve an inaccessible ASCII data
table referenced in an EML document? For instance, if a particular version of a
data set has been taken offline due to the discovery of major errors, how should 
the file access error be communicated to Kepler or some other Metacat/EML-savvy 
software agent (i.e. when they try to retrieve the old file based on a legacy 
EML document that hasn't been re-synced yet)?

The reason I'm asking is that I've been revising the GCE data distribution web
application to support stored cookies and more gracefully handle requests for
outdated or offline files, and I'd like to provide optimal support for both
interactive web clients and agents. I am currently using http and session
characteristics to distinguish these client types, and bouncing web clients to a
"contact the IM for assistance" web form on errors and returning a simple text 
message to agents, e.g. "Error: PLT-GCED-0409_1_2.TXT was not found on the 
GCE-LTER server (contact the GCE Information Manager <gcelter at uga.edu> for 
assistance)". If there is a common structured error message format (xml or text) 
supported by Kepler or other SEEK tools, though, I will use that instead.

Here are examples of what I'm doing now for invalid versions of data set tables 
(invalid data set accessions or missing files are handled similarly with 
different messages):

Invalid EML distribution URL (agent client):
http://gce-lter.marsci.uga.edu/lter/asp/db/send_file.asp?accession=PLT-GCED-0409&filename=PLT-GCED-0409_1_1.TXT&name=metacat-user&email=none&affiliation=LNO&notify=0

Invalid EML distribution URL (interactive client, using web session/cookie/login):
http://gce-lter.marsci.uga.edu/lter/asp/db/send_file.asp?accession=PLT-GCED-0409&filename=PLT-GCED-0409_1_2.TXT


One a related note, I've been archiving outdated but otherwise valid data sets
(e.g. those that have been updated to add an attribute or records) so that they
can be retrieved by URLs in legacy EML docs. However, not communicating the fact
that a more recent version of a data table is available seems to be a disservice
to users. Do you think it would be preferable to return an error or message if a 
more recent version of a data set exists, or just keep returning the old version 
as requested (if not taken offline) until the metadata is re-synced?

We are currently finalizing the "EML Best Practices for LTER Sites" document for 
general distribution, so if there is a consensus on these issues I'll add 
recommendations to the eml/dataset/dataTable/physical/distribution/online/url 
section.

Thanks.

Wade Sheldon
GCE-LTER Information Manager


____________________________________

Wade M. Sheldon
GCE-LTER Information Manager/SIMO Database Administrator
School of Marine Programs
University of Georgia
Athens, GA 30602-3636
Email: sheldon at uga.edu
WWW: http://gce-lter.marsci.uga.edu/lter/bios/wsheldon.htm


From sheldon at uga.edu  Tue Apr 12 17:04:09 2005
From: sheldon at uga.edu (Wade Sheldon)
Date: Tue, 12 Apr 2005 20:04:09 -0400
Subject: [eml-dev] Recommendations for reporting file access errors to
 software agents
In-Reply-To: <425C6007.4020802@uga.edu>
References: <E1DJI8I-0004DK-00@lternet.lternet.edu>	<42545DBE.4080104@nceas.ucsb.edu>
	<425C6007.4020802@uga.edu>
Message-ID: <425C61F9.7040907@uga.edu>

Oops, I incorrectly included a "correct" url as an example. Here's what I intended:

Invalid EML distribution URL (agent client):
http://gce-lter.marsci.uga.edu/lter/asp/db/send_file.asp?accession=PLT-GCED-0409&filename=PLT-GCED-0409_1_2.TXT&name=metacat-user&email=none&affiliation=LNO&notify=0

Note that if you paste this into a web browser after you have created a 
temporary session by logging in to download some other file (or trying the 
interactive link), or execute this url twice, it will switch to interactive 
mode. That's expected behavior.

--Wade



Wade Sheldon wrote:
> Matt and all,
> 
> What type of error message (content and formatting) do you think should be
> returned to a software agent that tries to retrieve an inaccessible ASCII data
> table referenced in an EML document? For instance, if a particular version of a
> data set has been taken offline due to the discovery of major errors, how should 
> the file access error be communicated to Kepler or some other Metacat/EML-savvy 
> software agent (i.e. when they try to retrieve the old file based on a legacy 
> EML document that hasn't been re-synced yet)?
> 
> The reason I'm asking is that I've been revising the GCE data distribution web
> application to support stored cookies and more gracefully handle requests for
> outdated or offline files, and I'd like to provide optimal support for both
> interactive web clients and agents. I am currently using http and session
> characteristics to distinguish these client types, and bouncing web clients to a
> "contact the IM for assistance" web form on errors and returning a simple text 
> message to agents, e.g. "Error: PLT-GCED-0409_1_2.TXT was not found on the 
> GCE-LTER server (contact the GCE Information Manager <gcelter at uga.edu> for 
> assistance)". If there is a common structured error message format (xml or text) 
> supported by Kepler or other SEEK tools, though, I will use that instead.
> 
> Here are examples of what I'm doing now for invalid versions of data set tables 
> (invalid data set accessions or missing files are handled similarly with 
> different messages):
> 
> Invalid EML distribution URL (agent client):
> http://gce-lter.marsci.uga.edu/lter/asp/db/send_file.asp?accession=PLT-GCED-0409&filename=PLT-GCED-0409_1_1.TXT&name=metacat-user&email=none&affiliation=LNO&notify=0
> 
> Invalid EML distribution URL (interactive client, using web session/cookie/login):
> http://gce-lter.marsci.uga.edu/lter/asp/db/send_file.asp?accession=PLT-GCED-0409&filename=PLT-GCED-0409_1_2.TXT
> 
> 
> One a related note, I've been archiving outdated but otherwise valid data sets
> (e.g. those that have been updated to add an attribute or records) so that they
> can be retrieved by URLs in legacy EML docs. However, not communicating the fact
> that a more recent version of a data table is available seems to be a disservice
> to users. Do you think it would be preferable to return an error or message if a 
> more recent version of a data set exists, or just keep returning the old version 
> as requested (if not taken offline) until the metadata is re-synced?
> 
> We are currently finalizing the "EML Best Practices for LTER Sites" document for 
> general distribution, so if there is a consensus on these issues I'll add 
> recommendations to the eml/dataset/dataTable/physical/distribution/online/url 
> section.
> 
> Thanks.
> 
> Wade Sheldon
> GCE-LTER Information Manager
> 
> 
> ____________________________________
> 
> Wade M. Sheldon
> GCE-LTER Information Manager/SIMO Database Administrator
> School of Marine Programs
> University of Georgia
> Athens, GA 30602-3636
> Email: sheldon at uga.edu
> WWW: http://gce-lter.marsci.uga.edu/lter/bios/wsheldon.htm
> 
> _______________________________________________
> Eml-dev mailing list
> Eml-dev at ecoinformatics.org
> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/eml-dev

-- 
____________________________________

Wade M. Sheldon
GCE-LTER Information Manager/SIMO Database Administrator
School of Marine Programs
University of Georgia
Athens, GA 30602-3636
Email: sheldon at uga.edu
WWW: http://gce-lter.marsci.uga.edu/lter/bios/wsheldon.htm


