<p>You could use the <a href="https://api.bacdive.dsmz.de/" rel="nofollow noreferrer">BacDive API</a>, or you could download the kgx formatted files from <a href="https://github.com/Knowledge-Graph-Hub/kg-microbe" rel="nofollow noreferrer">KG Microbe</a>.</p>

CC BY-SA 4.0
2024-03-31T15:57:33.467Z
2024-03-31T15:57:33.467Z
Chris Mungall
<p>let's say I have a list of organism names like the example below</p>
<pre><code>Achromobacter xylosoxidans
Acidithiobacillus ferrooxidans
Chloroflexus aurantiacus
Clostridium perfringens
Aquaspirillum arcticum
</code></pre>
<p>The goal is to identify the optimal growth conditions for each organism--meaning the optimal growth temperature and pressure. Obviously I can just google this information if the list is composed of a few organisms or even few tens of organisms. However, assuming that the list is too large, let's say several 100s of names, what would be an efficient means to gathering this information.</p>
<p>In searching for this info, I have not come across a database that has the information that I'm looking for in one place. Instead I find that this information is scattered across multiple sites, databases, scientific publications, protocols, etc. For each organism, I basically have to search through and extract this manually, and I was wondering if anyone can suggest some way to automate this. I am familiar with Python3, ideally I would accomplish this with python.</p>
<p>I though about implementing some sort of a web scraping solution, where I provide the name of the organism, as well as a few key words and see what happens. However, many times this data is not well tabulated and the name and whenever you do find information on the organism, you need to read to be able to interpret the information to get your answer...</p>
<p>maybe I'm not looking in the right place, or my approach to this problem is wrong/backwards/etc, any suggestions will help.</p>
<p>I haven't been able to find a centralized place to gather this information, that's why I posted here. The closest thing I've found is the <a href="https://atcc.org/" rel="nofollow noreferrer">ATCC</a>.</p>

CC BY-SA 4.0
2023-08-16T16:18:37.527Z
https://www.biostars.org/p/235851/
pippo1980
CC BY-SA 4.0
2023-08-16T16:20:48.957Z
yuo need to parse all of their product sheet, colored pdfs .....https://www.atcc.org/api/pdf/product-sheet?id=49176
pippo1980
<database><public-databases>
Gathering data on bacterial organism growth conditions
# Gathering data on bacterial organism growth conditions

(Asked by: username_0 on 2018-08-31)

let's say I have a list of organism names like the example below
Achromobacter xylosoxidans
Acidithiobacillus ferrooxidans
Chloroflexus aurantiacus
Clostridium perfringens
Aquaspirillum arcticum

The goal is to identify the optimal growth conditions for each organism--meaning the optimal growth temperature and pressure. Obviously I can just google this information if the list is composed of a few organisms or even few tens of organisms. However, assuming that the list is too large, let's say several 100s of names, what would be an efficient means to gathering this information.
In searching for this info, I have not come across a database that has the information that I'm looking for in one place. Instead I find that this information is scattered across multiple sites, databases, scientific publications, protocols, etc. For each organism, I basically have to search through and extract this manually, and I was wondering if anyone can suggest some way to automate this. I am familiar with Python3, ideally I would accomplish this with python.
I though about implementing some sort of a web scraping solution, where I provide the name of the organism, as well as a few key words and see what happens. However, many times this data is not well tabulated and the name and whenever you do find information on the organism, you need to read to be able to interpret the information to get your answer...
maybe I'm not looking in the right place, or my approach to this problem is wrong/backwards/etc, any suggestions will help.
I haven't been able to find a centralized place to gather this information, that's why I posted here. The closest thing I've found is the ATCC.

**Tags:** database, public-databases
> **Comments:**
> **username_1**: https://www.biostars.org/p/235851/  
> **username_1**: yuo need to parse all of their product sheet, colored pdfs .....https://www.atcc.org/api/pdf/product-sheet?id=49176  

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## 1 answers

### Answer by username_2 on 2024-03-31. Score: 1

You could use the [BacDive API](https://api.bacdive.dsmz.de/), or you could download the kgx formatted files from [KG Microbe](https://github.com/Knowledge-Graph-Hub/kg-microbe).


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