Answers.Body: <p>The <a href="https://gold.jgi.doe.gov/index" rel="nofollow noreferrer">GOLD database</a> can be used to retrieve a list of species names according to their Gram staining: go to the "<a href="https://gold.jgi.doe.gov/search" rel="nofollow noreferrer">Advanced search</a>" page and select the either "gram-" or "gram+" under "Organism Fields" -> "Gram Stain". Then on the results page click on the number under "Organisms". On the results page you can select to have 1000 results per page, meaning that you would need to do some manual work.</p>
  
  <p>I should add that as far as I know this information is based on what people submit when they register their genome projects, so I wouldn't expect this list to be curated or 100% accurate.</p>
  
  <p>If you have access to the genome of the species you are interested in (you could download a representative strain for each species using <a href="https://github.com/kblin/ncbi-genome-download" rel="nofollow noreferrer">ncbi-genome-download</a>), you could use <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192078/" rel="nofollow noreferrer">traitar</a>, which can predict the gram staining, among other interesting broad phenotypes.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-31T18:14:43.700Z
Answers.Text: Thanks for your help. I was thinking about downloading GOLD database data and use a program to find my required information. But I am unable to download the data. So can you please help me to do that.
Answers.UserDisplayName: Arijit Panda
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-01T07:25:31.130Z
Answers.Text: Is there any way to query the GOLD database programatically?
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-01T08:20:21.767Z
Answers.Text: No, their usage policy is in fact quite strict: "Downloading GOLD metadata by any means including web searches, downloadable reports, screen scraping, etc., is strictly prohibited without prior permission, if the purpose is to dissect, alter and store the GOLD data in a database (relational or text) and distribute to third parties/general public/collaborators."
Answers.UserDisplayName: mgalardini
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-31T13:23:21.527Z
Answers.LastActivityDate: 2017-09-01T08:27:33.743Z
Answers.LastEditDate: 2017-09-01T08:27:33.743Z
Answers.UserDisplayName: mgalardini
Answers.Body: <p><a href="https://msberends.github.io/AMR/reference/mo_property.html" rel="nofollow noreferrer">AMR R package</a> can assign gram staining based on taxonomy. See <code>mo_gramstain(x, language = get_AMR_locale(), ...)</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-09-23T21:24:23.113Z
Answers.LastActivityDate: 2022-09-23T21:24:23.113Z
Answers.UserDisplayName: fconstancias
Body: <p>I have a very long list of prokaryote organism names. I would like to know their <strong>gram staining</strong> (gram positive or gram negative) information.</p>
  
  <p>Please let me know if there is any database that keeps this information.</p>
  
  <p>I am also trying to find a program that can find gram staining information via organism name only as my organism list is long.</p>
  
  <p>Edit: for each species the NCBI taxonomy lineage is also available</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-31T13:13:30.480Z
Comments.Text: You only have their names, or you also have their genomes?
Comments.UserDisplayName: mgalardini
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-31T13:26:07.740Z
Comments.Text: I have only their names, I can able find their taxonomy lineage using NCBI taxonomy database if that helps me to find the gram staining.
Comments.UserDisplayName: Arijit Panda
Tags: <database><public-databases><microbiology>
Title: How can I work out gram staining information from the species name?
ThreadText: # How can I work out gram staining information from the species name?
  
  (Asked by: username_0 on 2017-08-31)
  
  I have a very long list of prokaryote organism names. I would like to know their **gram staining** (gram positive or gram negative) information.
  
  Please let me know if there is any database that keeps this information.
  
  I am also trying to find a program that can find gram staining information via organism name only as my organism list is long.
  
  Edit: for each species the NCBI taxonomy lineage is also available
  
  **Tags:** database, public-databases, microbiology
  
  > **Comments:**
  > **username_1**: You only have their names, or you also have their genomes?  
  > **username_0**: I have only their names, I can able find their taxonomy lineage using NCBI taxonomy database if that helps me to find the gram staining.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2017-08-31. Score: 3
  
  The [GOLD database](https://gold.jgi.doe.gov/index) can be used to retrieve a list of species names according to their Gram staining: go to the "[Advanced search](https://gold.jgi.doe.gov/search)" page and select the either "gram-" or "gram+" under "Organism Fields" -> "Gram Stain". Then on the results page click on the number under "Organisms". On the results page you can select to have 1000 results per page, meaning that you would need to do some manual work.
  
  I should add that as far as I know this information is based on what people submit when they register their genome projects, so I wouldn't expect this list to be curated or 100% accurate.
  
  If you have access to the genome of the species you are interested in (you could download a representative strain for each species using [ncbi-genome-download](https://github.com/kblin/ncbi-genome-download)), you could use [traitar](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192078/), which can predict the gram staining, among other interesting broad phenotypes.
  
  > **Comments:**
  > **username_0**: Thanks for your help. I was thinking about downloading GOLD database data and use a program to find my required information. But I am unable to download the data. So can you please help me to do that.  
  > **username_2**: Is there any way to query the GOLD database programatically?  
  > **username_1**: No, their usage policy is in fact quite strict: "Downloading GOLD metadata by any means including web searches, downloadable reports, screen scraping, etc., is strictly prohibited without prior permission, if the purpose is to dissect, alter and store the GOLD data in a database (relational or text) and distribute to third parties/general public/collaborators."  
  
  ---
  
  ### Answer by username_3 on 2022-09-23. Score: 1
  
  [AMR R package](https://msberends.github.io/AMR/reference/mo_property.html) can assign gram staining based on taxonomy. See `mo_gramstain(x, language = get_AMR_locale(), ...)`.
  
  
  ---
  
  