change metadata formatting from dbase

[ackermag]

• GENDER to sex, calculate BMI from weight and height, remove one of these:MIGRAINEMEDS or MIGRAINE_MEDS, change all text entries to lower case

[douginator2000]

Please be more specific - what are we talking about specifically here?
Where in the app?

On Fri, Jul 5, 2013 at 11:27 AM, ackermag notifications@github.com wrote:

• GENDER to sex, calculate BMI from weight and height, remove one of
  these:MIGRAINEMEDS or MIGRAINE_MEDS, change all text entries to lower case

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/460
.

Doug Wendel
Professional Research Associate
University of Colorado at Boulder
Department of Chemistry and Biochemistry, Knight Lab
303-641-5442
wendel@colorado.edu

[ackermag]

The download you provide me from the AGP dbase always needs manual
curation.

• Is there any way that the entries in the fields that come from the
  download can be lower case for most of the participant entered data?
• There are 2 identical columns generated MIGRAINE_MEDS and MIGRAINEMEDS -
  seems like duplication.
• Can you generate BMI before download from height, weight?

I don't know where in the app
Gail

On Fri, Jul 5, 2013 at 11:28 AM, Doug Wendel notifications@github.comwrote:

Please be more specific - what are we talking about specifically here?
Where in the app?

On Fri, Jul 5, 2013 at 11:27 AM, ackermag notifications@github.com
wrote:

• GENDER to sex, calculate BMI from weight and height, remove one of
  these:MIGRAINEMEDS or MIGRAINE_MEDS, change all text entries to lower
  case

—
Reply to this email directly or view it on GitHub<
https://github.com/qiime/qiime_web_app/issues/460>
.

Doug Wendel
Professional Research Associate
University of Colorado at Boulder
Department of Chemistry and Biochemistry, Knight Lab
303-641-5442
wendel@colorado.edu

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/460#issuecomment-20530188
.

Gail Ackermann
Knight Lab UCB 596
University of Colorado
Boulder

[douginator2000]

Gail, can you tell me specifically what fields should be lower-case?

[douginator2000]

I'm also working on the mappings between "site_sampled" and the corresponding UBERON/ENVO terms. Can you tell me what should be filled out for env_matter, env_feature, and env_biome (and any other standard fields) we can directly map for a human?

E.g. for a human stool sample, what values for each of those fields?

[ackermag]

sex (Gender)
SUPPLEMENTS_FIELDS PETS PET_CONTACT PET_LOCATIONS RELATIONS

On Mon, Jul 8, 2013 at 12:15 PM, Doug Wendel notifications@github.comwrote:

Gail, can you tell me specifically what fields should be lower-case?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/460#issuecomment-20625039
.

Gail Ackermann
Knight Lab UCB 596
University of Colorado
Boulder

[ackermag]

The following fields should be lower case:

sex (GENDER)
SUPPLEMENTS_FIELDS RELATIONS PET_LOCATIONS PET_CONTACT PETS
MIGRAINE_MEDICATIONS GENERAL_MEDS DIET_RESTRICTIONS
DIABETES_MEDICATIONS ANTIBIOTIC_MEDS ROOMMATES PRIMARY_VEGETABLE
PRIMARY_CARB
FOODALLERGIES_OTHER_TEXT
CONTRACEPTIVES
ANTIBIOTIC_CONDITION
For stool samples we enter:
body_habitat UBERON:feces;
body_site UBERON:feces;
body product UBERON:feces;
env_biome:
ENVO:human-associated habitatenv_feature:
ENVO:human-associated habitat
env_matter:
ENVO:feces
Gail

On Mon, Jul 8, 2013 at 12:15 PM, Doug Wendel notifications@github.comwrote:

Gail, can you tell me specifically what fields should be lower-case?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/460#issuecomment-20625039
.

Gail Ackermann
Knight Lab UCB 596
University of Colorado
Boulder