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qiime / qiime_web_app

QIIME, EMP and American Gut Web Application
www.microbio.me/qiime
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change metadata formatting from dbase #460

Open ackermag opened 11 years ago

ackermag commented 11 years ago
douginator2000 commented 11 years ago

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/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

ackermag commented 11 years ago

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

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/qiime/qiime_web_app/issues/460#issuecomment-20530188 .

Gail Ackermann Knight Lab UCB 596 University of Colorado Boulder

douginator2000 commented 11 years ago

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

douginator2000 commented 11 years ago

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 commented 11 years ago

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/qiime/qiime_web_app/issues/460#issuecomment-20625039 .

Gail Ackermann Knight Lab UCB 596 University of Colorado Boulder

ackermag commented 11 years ago

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/qiime/qiime_web_app/issues/460#issuecomment-20625039 .

Gail Ackermann Knight Lab UCB 596 University of Colorado Boulder