In BATMAN-TCM, the query TCM formula/herb will be first transferred into a list of compositive compounds based on the formula-herb-ingredient association data collected and integrated by TCMID database, and then for each ingredient, candidate targets will be predicted based on our target prediction method (see details about the method in Tutorials).
Thank you very much for your comments!
Thanks for your question. The ingredient list of the formula and herb are backed by TCMID data.
The formula-herb-ingredient association relationships in BATMAN-TCM are backed by TCMID database, including 46914 formulas and 8159 herbs. For those formulas or herbs not backed by TCMID database, you can input the herb list of your formula or the compound list of your formula/herb to analyze the herb/formula.
Sorry for the late reply. Thanks for your comments. Yes, now batman-tcm website can only analyze no more than 4 herbs at the same time. If you want to compare >4 herbs, now only by submitting several times can you achieve it. We are also considering improving this.
Sorry for the late reply. Thanks for your comments. I guess that maybe these missed herbs in fact are not in our background database. For these herbs not in our database, you can input their compositive compound lists to analyze them. Welcome further communication by email (email@example.com) at any time.
For a compound not in the PubChem database, you can submit its chemical structure of InChI format by the input type of "compound list". If you have a compound represented by other types of format, you can use OpenBabel to transfer it into InChI. Welcome further communication by firstname.lastname@example.org at any time.
Sorry, currently there is no API for BATMAN-TCM.
Sorry for the late reply. For the herb not in our database, you can input the compound list of the herb using the "compound list" input type to analyze it. Welcome further timely communication by email@example.com .
Sorry for the late reply! Thanks for your suggestion. Because of the backstage mechanism of our website, lower cutoff will significantly low the speed of our website. However, the downloadable target prediction results on the result page indeed include all predicted targets without cutoff limitation. Welcome further communication by firstname.lastname@example.org
Thanks for your comments. Last update: Jan. 2016
Thanks for your question. As I know, recently TCMID database has been updated into version 2. But unfortunately our backstage database has not been updated timely as the update of TCMID. I think this may lead to your question. Facing this condition, you can use the input type of "compound list" to input the structural data of your ingredient list to do the following analyses by BATMAN-TCM. And we will also update our backstage data as soon as possible. Welcome further communication by email@example.com
Thank you for the use. There is indeed a bug in this function which we will amend it soon. But if you download this graph, the downloaded graph will give the names of nodes. Please try! Thank you!
I am so sorry. There is indeed a bug here. We will fix it soon
Thanks for your comments. Just recently, we obtain a new funding. We plan to update BATMAN soon.
Sorry for the late reply. Owing to some limitation such as hardware, currently only a network containing no more than 400 nodes can been presented in BATMAN-TCM. Recently the network download function indeed doesn't work well. We will fix it soon.
Sorry for the late reply. Welcome further communication by firstname.lastname@example.org, by which you will obtain faster reply. BATMAN-TCM does provide comparison function of different herbs by the “Add one cluster” button on the homepage and also provide the venn graph of target sets of different herbs. But unfortunately currently we don’t provide the download function of the venn graph. You can “PrtSc” it. Recently we plan to improve BATMAN, and the download function will be provided. Thank you for your suggestion.
Yes, BATMAN-TCM provides the comparison analysis function between multiple different herbs. Compared with "one by one" analyses results, more results for comparison will be provided including venn graph between target sets of different herbs, KEGG pathway graph in which targets of different herbs will be highlighted with different colors.
Now the bug about "Download" has been fixed. Please try it again!
Thanks for your comments. Indeed as you said different ingredients can interact with each other. However, owing to the lack of the related data, BATMAN-TCM currently doesn't collect this data. Under the condition of insufficiency of the related data, BATMAN-TCM supports customized-input. Based on herb-specific prior knowledge, you can use its active ingredients, ingredients detected in plasma, metabolites of original constituents, even products from the interactions between ingredients or something like those that really contribute to its therapeutic effects as the input to further predict targets. As we said in the m.s. of BATMAN-TCM, "there are still many uncertainties in currently available data that BATMAN-TCM depends on, such as the incomplete definition of active composition of each formula, the absence of the quantitative information of components in each formula etc.. Therefore, we advise and encourage users to (!!!!!! To Q22)
We are sorry. Currently BATMAN-TCM doesn't support users to manually change the node name size. The size is automatically changed as the node size. We suggest that you can edit your figure using another tool. In the next version, we maybe consider improve this. Thanks.
Therefore, we advise and encourage users to take full advantage of the function of user-customized input of the ingredient list, and meanwhile combine the analysis results given by BATMAN-TCM with the biological knowledge and professional experience to make the most proper judgment. "
Yes. Thanks a lot for you suggestion. We will show the update time on the homepage.
Sorry for the late reply. If you zoom in, you will see the gene name. Sorry for the inconvenience.
Thank you for your comments! Sorry, currently the function you asked is not supported!
It depends on the length of your input list. About 10 hours for 150 compounds.
We provide the predicted target list for each ingredient compound which can be downloaded. You can compare two compounds' target lists to find the common.
Maybe these compounds have very similar structures? You can send an example to me, and I will check it. (email@example.com)
Can you send an example to me (firstname.lastname@example.org), and I will check it.
The fomula's herbal composition data are from TCMID database. We didn't collect the related data by ourseleves. Facing this problem, you can use the herbal list as the input to perform the following analyses.
Sorry for the problem. We will fix it soon. Try it again after a few days.
Hi, I have test this function and it seems work well. Can you send the URL with wrong to me, and I will check it. (email@example.com)
Sorry for the problem. Try another web browser.
Sorry for the bug. Actually if you zoom in enough, you can see the gene name. But indeed the gene names are too small. We will improve it as soon as possible.
Sorry. I can send the data to you. Please contact me (firstname.lastname@example.org)
The function works well. You can try another kind of web browser or another computer.
In BATMAN-TCM, ingredient-herb association data indeed are from TCMID. You can use TCMID data directly.
If the P-value<=cutoff you have set, it will be marked in red.
In BATMAN-TCM, enrichment ratio=(m/n)/(M/N). N=the whole genome; M=the number of genes in the pathway; n=the number of targets; m=the number of targets participating the pathway. Maybe different versions of KEGG pathway data have lead to the inconsistence.
I think that "choose a very large score cutoff" is a solution for your need.
Attention: You might obtain late reply here. If a fast reply is required, please use email@example.com. Thank you!
Contact: Zhongyang Liu, firstname.lastname@example.org, Beijing Proteome Research Center, Beijing, China.