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From: "Boyle, Bradley L - (bboyle)" <bboyle@email.arizona.edu>

To: Aaron Marcuse-Kubitza <aaronmk@nceas.ucsb.edu>

CC: Martha Narro <narro@iplantcollaborative.org>, BIEN Database Working Group

	<bien-db@iplantcollaborative.org>

Subject: Qualitative validations for traits, plus revised task list

Thread-Topic: Qualitative validations for traits, plus revised task list

Thread-Index: AQHPFs40E9fYzYyVSkyRktxAppKEww==

Date: Tue, 21 Jan 2014 17:28:31 +0000

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Hi Aaron,

Attached are the two sets of quantitative validations for traits: one set o=

f mysql queries against the original table in BIEN2, and another set of pos=

tgres queries against the trait table in BIEN3 (vegbien). There are eight q=

ueries total. The BIEN2 queries are complete; however, I will need you to w=

rite the BIEN3 queries 5, 6 and 8. The latter queries involve taxon names a=

nd I am not confident that I understand how you form the verbatim taxon nam=

e in vegbien. Note that the taxon name includes the family ONLY IF the genu=

s (or lower taxon) is unknown.

Please send the BIEN3 queries to me after you have written the missing quer=

ies. That will help me to understand how you are handling taxonomy so I can=

 write these queries myself in the future.

In the process of writing these validations, I discovered a few issues with=

 the trait data that needed to be fixed. After you have completed the queri=

es, but before you run the validations, please reload the trait data from t=

he original.

Also, in the process of writing the SALVIAS validations (which I sent to yo=

u on the weekend) I also discovered some issues. I fixed these as well. The=

y are all relatively minor issues, but will nonetheless cause the quantitat=

ive validations to fail when you run them without reloading the revised dat=

a. So, please reload the SALVIAS data before running the SALVIAS validation=

s.

Because of the need to reload data suggests some changes to your task list =

from our last meeting. Apart from step 1, I would like you to complete the =

trait validations first as they are simplest. Please complete the following=

 tasks in the order of priority indicated:

1. SALVIAS data contributors

        Make any necessary revisions to vegbien schema and scripts to accom=

modate  the SALVIAS plot and project data contributors, as described in my =

"High priority tasks" email message of Dec. 17/18. Do not reload the SALVIA=

S data yet; you will do that later  in step 3.

2. Trait validations

        2.a. Complete the queries for the Trait validations against vegbien=

.

        2.b.     Compare carefully the two sets of queries to ensure they p=

rovide identical output (assuming identical content). Check especially that=

 aliases and sort orders are identical. Revise if necessary. Send the finis=

hed queries to me when you are done.

        2.c. Automate the Trait validations using the diff approach you hav=

e proposed. The automation validation process should produce a report detai=

ling which queries passed and which failed.

        2.d. Reload the trait data from the original table in BIEN2.

        2.e. Run the trait validations and report the results to Martha and=

 myself.

3. SALVIAS validations

        3.a. Complete the queries for the SALVIAS validations against vegbi=

en. The missing queries either involve taxon names or subplots, or infer th=

e observation method (individuals, species counts, percent cover, etc).

        3.b.     Compare carefully the two sets of queries to ensure they p=

rovide identical output (assuming identical content). Check especially that=

 aliases and sort orders are identical. Revise if necessary. Send the finis=

hed queries to me when you are done.

        3.c. Automate the SALVIAS validations using the diff approach you h=

ave proposed. The automation validation process should produce a report det=

ailing which queries passed and which failed.

        3.d. Reload the SALVIAS data from the original table in BIEN2.

        3.e. Run the SALVIAS validations and report the results to Martha a=

nd myself.

Don't hesitate to ask me right away if you have questions. These validation=

s are not simple and perfecting them may require a bit of experimentation a=

nd discussion. The validations themselves will likely uncover problems that=

 will need to be fixed. However, the effort we put in now will pay off in t=

he long run. Extending these queries to other data sources should get faste=

r as we go along, and we can be confident about releasing the data once it =

passes validation.

Thanks,

Brad

--_000_D9E5B32B49BA4419A2A07F70D706D8AEemailarizonaedu_

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Content-ID: <DDA3479128EB2242B1E34FC448D35A6A@email.arizona.edu>

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<head>

<meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Dus-ascii"=

>

</head>

<body>

<div class=3D"BodyFragment"><font size=3D"2"><span style=3D"font-size:10pt;=

">

<div class=3D"PlainText">Hi Aaron,<br>

<br>

Attached are the two sets of quantitative validations for traits: one set o=

f mysql queries against the original table in BIEN2, and another set of pos=

tgres queries against the trait table in BIEN3 (vegbien). There are eight q=

ueries total. The BIEN2 queries

 are complete; however, I will need you to write the BIEN3 queries 5, 6 and=

 8. The latter queries involve taxon names and I am not confident that I un=

derstand how you form the verbatim taxon name in vegbien. Note that the tax=

on name includes the family ONLY

 IF the genus (or lower taxon) is unknown.<br>

<br>

Please send the BIEN3 queries to me after you have written the missing quer=

ies. That will help me to understand how you are handling taxonomy so I can=

 write these queries myself in the future.<br>

<br>

In the process of writing these validations, I discovered a few issues with=

 the trait data that needed to be fixed. After you have completed the queri=

es, but before you run the validations, please reload the trait data from t=

he original.<br>

<br>

Also, in the process of writing the SALVIAS validations (which I sent to yo=

u on the weekend) I also discovered some issues. I fixed these as well. The=

y are all relatively minor issues, but will nonetheless cause the quantitat=

ive validations to fail when you

 run them without reloading the revised data. So, please reload the SALVIAS=

 data before running the SALVIAS validations.<br>

<br>

Because of the need to reload data suggests some changes to your task list =

from our last meeting. Apart from step 1, I would like you to complete the =

trait validations first as they are simplest. Please complete the following=

 tasks in the order of priority

 indicated:<br>

<br>

1. SALVIAS data contributors<br>

<br>

        Make any necessary revisions to =

vegbien schema and scripts to accommodate  the SALVIAS plot and projec=

t data contributors, as described in my "High priority tasks" ema=

il message of Dec. 17/18. Do not reload the SALVIAS data yet; you will do t=

hat later 

 in step 3.<br>

<br>

2. Trait validations<br>

<br>

        2.a. Complete the queries for th=

e Trait validations against vegbien.<br>

        2.b.     Com=

pare carefully the two sets of queries to ensure they provide identical out=

put (assuming identical content). Check especially that aliases and sort or=

ders are identical. Revise if necessary. Send the finished queries to me wh=

en you are done.<br>

        2.c. Automate the Trait validati=

ons using the diff approach you have proposed. The automation validation pr=

ocess should produce a report detailing which queries passed and which fail=

ed.<br>

        2.d. Reload the trait data from =

the original table in BIEN2.<br>

        2.e. Run the trait validations a=

nd report the results to Martha and myself.<br>

<br>

3. SALVIAS validations<br>

        3.a. Complete the queries for th=

e SALVIAS validations against vegbien. The missing queries either involve t=

axon names or subplots, or infer the observation method (individuals, speci=

es counts, percent cover, etc).

<br>

        3.b.     Com=

pare carefully the two sets of queries to ensure they provide identical out=

put (assuming identical content). Check especially that aliases and sort or=

ders are identical. Revise if necessary. Send the finished queries to me wh=

en you are done.<br>

        3.c. Automate the SALVIAS valida=

tions using the diff approach you have proposed. The automation validation =

process should produce a report detailing which queries passed and which fa=

iled.<br>

        3.d. Reload the SALVIAS data fro=

m the original table in BIEN2.<br>

        3.e. Run the SALVIAS validations=

 and report the results to Martha and myself.<br>

<br>

Don't hesitate to ask me right away if you have questions. These validation=

s are not simple and perfecting them may require a bit of experimentation a=

nd discussion. The validations themselves will likely uncover problems that=

 will need to be fixed. However,

 the effort we put in now will pay off in the long run. Extending these que=

ries to other data sources should get faster as we go along, and we can be =

confident about releasing the data once it passes validation.<br>

<br>

Thanks,<br>

Brad<br>

<br>

</div>

</span></font></div>

<div class=3D"BodyFragment"><font size=3D"2"><span style=3D"font-size:10pt;=

">

<div class=3D"PlainText"><br>

<br>

<br>

</div>

</span></font></div>

</body>

</html>

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