<p>I really don't see what we can add that the errors aren't telling you: the IDs you are looking for aren't present in the databases you are using. One obvious issue I can see is that you say you use NCBI gene IDs, but then your error shows text, not numbers.You have only given us images, and I am not willing to copy each ID one by one, so I just checked &quot;Ano9&quot;. <a href="https://www.ncbi.nlm.nih.gov/gene/338440" rel="nofollow noreferrer">As you can see</a> if you search NCBI for Ano9, the human Ano9 gene's ID is 338440, but you seem to have entered <code>Ano9</code> instead.</p>
<p>So, make sure you use the same kind of ID, you can't mix and match. And make sure you use up to date IDs that exist in the databases you want to work with. For more help, edit your question and give us the actual list of things that don't work. Not a photograph of it that we need to transcribe.</p>

CC BY-SA 4.0
2024-07-15T16:30:45.047Z
2024-07-15T16:30:45.047Z
terdon
<p>I'm new to using metscape and am having some trouble with entering my compound IDs and gene IDs into the system. When I enter my compound IDs as KEGG IDs, around a quarter of my data goes unrecognized by the system and shows up as &quot;missing elements.&quot; Something similar happens with my gene data as well. I was wondering if this is typical? I'm just not sure as I fear that I'm not analyzing the entire set of the data that I want to.</p>
<p>edit: Thank you for your suggestions and clarifying questions! To be more specific, I have a list of KEGG id's that I'm trying to input into the Compound input ID's in Metscape. Using an example of just a few of the compounds that I'm trying to input, when I &quot;Add&quot; the samples into the compound list box and hit &quot;OK&quot;, many of my samples are recognized by the system as shown here :</p>
<p><a href="https://i.sstatic.net/Olj94MW1.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Olj94MW1.png" alt="example list of working compounds" /></a></p>
<p>However, I consistently get a &quot;Missing Error&quot; message of data that cannot be found in the database, as shown here:
<a href="https://i.sstatic.net/GZYkbxQE.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/GZYkbxQE.png" alt="example list of non-working compound" /></a></p>
<p>I'm having a bit of trouble understanding why certain KEGG compounds are not being recognized. In this example I only imput a few compounds, so there was only one missing element. However, when I input my list that included hundreds of compounds, around a quarter of my data shows up as missing elements.</p>
<p>I face a similar problem when I attempt to input my genes into the database. For example, when I put in a small subset of genes into the system, only some are recognized:
<a href="https://i.sstatic.net/Dd1ugis4.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Dd1ugis4.png" alt="example of genes working" /></a></p>
<p>while many go unrecognized: <a href="https://i.sstatic.net/pBDmry7f.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/pBDmry7f.png" alt="example of genes not working" /></a></p>
<p>For the genes, I understand that this may be because many of the genes I'm inputting don't code for metabolic enzymes?</p>
<p>Does anyone have any insight into why so much of my data is going unrecognized by the system or how I can get more of my data to be recognized by the database?</p>
<p>Thank you!</p>

CC BY-SA 4.0
2024-07-12T03:22:02.857Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2024-07-12T08:16:11.447Z
Please [edit] your question and give us an example of your input data. Ideally, some identifiers that are recognized as well as some that are not. Make sure to tell us what kind of gen ID you are using (there are dozens of different types of gene ID). Have you checked any of these IDs manually? If you look the missing element up in KEGG, for instance, do you find it?
terdon
CC BY-SA 4.0
2024-07-12T21:58:46.930Z
You've mentioned a partial error, `missing elements`; please show the full error as copy/pasted text if possible, or a screenshot if copy/pasting is not possible. Including the first few lines of your data, or a subset which demonstrates this error, is incredibly helpful as well.
gringer
<identifiers><kegg>
KEGG IDs and gene IDs going unrecognized in Cytoscape metscape software
# KEGG IDs and gene IDs going unrecognized in Cytoscape metscape software

(Asked by: username_0 on 2024-07-11)

I'm new to using metscape and am having some trouble with entering my compound IDs and gene IDs into the system. When I enter my compound IDs as KEGG IDs, around a quarter of my data goes unrecognized by the system and shows up as "missing elements." Something similar happens with my gene data as well. I was wondering if this is typical? I'm just not sure as I fear that I'm not analyzing the entire set of the data that I want to.

edit: Thank you for your suggestions and clarifying questions! To be more specific, I have a list of KEGG id's that I'm trying to input into the Compound input ID's in Metscape. Using an example of just a few of the compounds that I'm trying to input, when I "Add" the samples into the compound list box and hit "OK", many of my samples are recognized by the system as shown here :

[![example list of working compounds](https://i.sstatic.net/Olj94MW1.png)](https://i.sstatic.net/Olj94MW1.png)

However, I consistently get a "Missing Error" message of data that cannot be found in the database, as shown here:
[![example list of non-working compound](https://i.sstatic.net/GZYkbxQE.png)](https://i.sstatic.net/GZYkbxQE.png)

I'm having a bit of trouble understanding why certain KEGG compounds are not being recognized. In this example I only imput a few compounds, so there was only one missing element. However, when I input my list that included hundreds of compounds, around a quarter of my data shows up as missing elements.

I face a similar problem when I attempt to input my genes into the database. For example, when I put in a small subset of genes into the system, only some are recognized:
[![example of genes working](https://i.sstatic.net/Dd1ugis4.png)](https://i.sstatic.net/Dd1ugis4.png)

while many go unrecognized: [![example of genes not working](https://i.sstatic.net/pBDmry7f.png)](https://i.sstatic.net/pBDmry7f.png)

For the genes, I understand that this may be because many of the genes I'm inputting don't code for metabolic enzymes?

Does anyone have any insight into why so much of my data is going unrecognized by the system or how I can get more of my data to be recognized by the database?

Thank you!

**Tags:** identifiers, kegg
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: Please [edit] your question and give us an example of your input data. Ideally, some identifiers that are recognized as well as some that are not. Make sure to tell us what kind of gen ID you are using (there are dozens of different types of gene ID). Have you checked any of these IDs manually? If you look the missing element up in KEGG, for instance, do you find it?  
> **username_3**: You've mentioned a partial error, `missing elements`; please show the full error as copy/pasted text if possible, or a screenshot if copy/pasting is not possible. Including the first few lines of your data, or a subset which demonstrates this error, is incredibly helpful as well.  

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## 1 answers

### Answer by username_2 on 2024-07-15. Score: 0

I really don't see what we can add that the errors aren't telling you: the IDs you are looking for aren't present in the databases you are using. One obvious issue I can see is that you say you use NCBI gene IDs, but then your error shows text, not numbers.You have only given us images, and I am not willing to copy each ID one by one, so I just checked "Ano9". [As you can see](https://www.ncbi.nlm.nih.gov/gene/338440) if you search NCBI for Ano9, the human Ano9 gene's ID is 338440, but you seem to have entered `Ano9` instead.

So, make sure you use the same kind of ID, you can't mix and match. And make sure you use up to date IDs that exist in the databases you want to work with. For more help, edit your question and give us the actual list of things that don't work. Not a photograph of it that we need to transcribe.


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