1  How to predict herbs or fumula's target?      Asked by Sally at 2014-12-31 17:20:55    

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).

2  This is a powerful bioinformatics tool.     Asked by jeffery at 2014-12-31 23:05:18    

Thank you very much for your comments!

3  How do you obtain the ingredient list of the submitted formula or herb?     Asked by Wang at 2015-01-06 15:41:58    

Thanks for your question. The ingredient list of the formula and herb are backed by TCMID data.

4  I find the interested formula or herb doesn’t exist in your database.      Asked by Guest at 2015-01-14 10:45:03    

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.

5  It's a great web! But how can we define more than four herbs or cluster in the first step? It seems that it can be typed in only four or less?      Asked by tutu at 2016-11-17 22:34:17    

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.

6  There must be something wrong with this web, When typing combination of mutiple herbs, the results always miss a few of them! And this did not happen before when I used this web      Asked by aa at 2016-12-20 19:20:40    

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 (liuzy1984@164.com) at any time.

7  How to analyze a compound that doesn't exist in the PUBCHEM database?     Asked by M at 2017-03-22 16:25:00    

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 liuzy1984@163.com at any time.

8  Is there any API for BATMAN-TCM     Asked by LiYang at 2017-03-23 22:27:47    

Sorry, currently there is no API for BATMAN-TCM.

9  There is no data on Boussingaultia gracilis Miers. var. baselloides Bail?teng san qi) in the database?     Asked by liu lei at 2017-04-10 23:06:15    

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 liuzy1984@163.com .

10  Can you set the Score cutoff down to 5 or lower? As some of my search show no result if the value is 10. Thank you.     Asked by WL at 2017-09-06 20:48:59    

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 liuzy1984@163.com

11  This site provides a great help to our study. However, most of the magazines required to provide the website version or last update time, I didn't find the relevant information on this website. We hope you could release the information of the version or last update time to public. Thank you very much.     Asked by Yanan He at 2017-12-23 11:14:37    

Thanks for your comments. Last update: Jan. 2016

12  your database show me only a little ingredients when i input a herb's name.and the database showed that the other ingredients don't have structural information and thus their targets cannot be predicted.But when i search the same herb in TCMID(http://www.megabionet.org/tcmid/ ) it showed much more ingredients of this herb that has structural.so this got me bothered.i just don't know if the search result in your database is enough or not.     Asked by Liu BT at 2018-04-03 18:22:48    

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 liuzy1984@163.com

13  I like the web.But why dont the "Ingredient-target-pathway/disease network" show the name of each part?only show the shape. THANK YOU.     Asked by Liu Weiwei at 2018-05-09 16:48:16    

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!

14  I like the web.But why I downloaded the "Ingredient-target-pathway/disease network" at whole network view, the downloaded graph will not give the names of nodes. THANK YOU.      Asked by Crista at 2018-08-16 18:42:41    

I am so sorry. There is indeed a bug here. We will fix it soon

15  Whether update the databases? Since most of databases were dowloaded 3 or 4 years ago according to "Liu Z, Guo F, Wang Y, Li C, Zhang X, Li H, Diao L, Gu J, Wang W, Li D, He F. BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine. Sci Rep. 2016, 6:21146."     Asked by Joyce at 2018-08-17 14:25:04    

Thanks for your comments. Just recently, we obtain a new funding. We plan to update BATMAN soon.

16  How to set the appropriate P value to view the whole net work view,and why can't I download the image after I click the export button?     Asked by alpha at 2018-08-21 15:03:00    

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.

17  How to get a venn diagram to compare between the predicted target sets of different clusters?     Asked by Amelia at 2018-09-27 10:50:53    

Sorry for the late reply. Welcome further communication by liuzy1984@163.com, 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.

18  Can I analyze several herbs at the same time? What is the difference from that I analyze one by one?      Asked by Lynn at 2018-10-28 21:38:02    

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.

19  Thanks for sharing. Except I cannot download those files under 'Download' tag. Could you please share these two files listed? Thanks in advance     Asked by Yakun Chen at 2018-12-10 10:18:09    

Now the bug about "Download" has been fixed. Please try it again!

20  My sincere congratulations to the team that took upon the monumental task of creating this database. I hope you will keep updating and improving it continuously and that researchers such as myself may keep using it for free. As it is common knowledge, ingredients from different herbs in a single formula will interact with each other (even ingredients within a single herb will too). How do you take that into account in predicting the biological targets and performing the enrichment analyses?      Asked by Carlos at 2019-01-10 21:44:57    

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)

21  I like the web.But How can i change the point sizes of the names of nodes?the sizes in downloaded graph is too small. THANK YOU.      Asked by Xia at 2019-01-22 19:20:28    

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.

22  From Answer to Q20     Asked by Zhongyang Liu at 2019-01-23 09:37:58    

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. "

23  The web helps a lot, thank you very much. There is a question that I'm not sure the time you update the website. I suggest that you can show the latest update time on the homepage so that users can see it directly. From the answers above, is 2016-01 still the last update time?     Asked by Jetty Wang at 2019-02-14 23:04:22    

Yes. Thanks a lot for you suggestion. We will show the update time on the homepage.

24  I like the web.But why in Ingredient-target-pathway/disease network,I cannot see genes name.THANK YOU.     Asked by tina at 2019-02-28 17:32:21    

Sorry for the late reply. If you zoom in, you will see the gene name. Sorry for the inconvenience.

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Contact: Zhongyang Liu, liuzy1984@163.com, Beijing Proteome Research Center, Beijing, China.