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.
25 Thank you very much for your analysis platform. It is really excellent.?I would like to ask if there is a prescription-target-pathway/disease network for a single disease. Asked by Listening at 2019-11-05 07:06:13
Thank you for your comments! Sorry, currently the function you asked is not supported!
26 How soon can I receive an email with the results of the compound analysis? Asked by Jenny at 2019-11-30 12:25:35
It depends on the length of your input list. About 10 hours for 150 compounds.
27 How to search for common targets of two compounds? Asked by Jenny at 2019-12-05 17:55:19
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.
28 The number, type, and score of targets predicted by many different compounds are completely the same. What is the reason and how to deal with it? Asked by bhs at 2019-12-23 13:49:35
Maybe these compounds have very similar structures? You can send an example to me, and I will check it. (liuzy1984@163.com)
29 download the visualiztion speed so slow, render speed should be improved. excel data some are diferent from the website data, how do this? really strange! Asked by xiaozhe at 2019-12-24 13:53:48
Can you send an example to me (liuzy1984@163.com), and I will check it.
30 Why some formulers'herbs is different in our book? Asked by jia at 2020-01-24 01:49:57
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.
31 cannot download BATMAN-TCM data in Download tab, it shows "file not found" Asked by Zhou Li at 2020-01-30 22:18:27
Sorry for the problem. We will fix it soon. Try it again after a few days.
32 I cannot open up the zip of BATMAN-TCM data,especially the Target Prediction Result after Download, it shows that the zip is wrong. Asked by Hongzheng Li at 2020-02-06 00:27:40
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. (liuzy1984@163.com)
33 I think there are some problems with the network visualization, the node names are too small. Asked by zbw at 2020-02-21 14:45:24
Sorry for the problem. Try another web browser.
34 The web is great.But why in Ingredient-target-pathway/disease network,I cannot see genes name?Although I zoom in, still donnot see the name.Please reply as soon as possible?THANK YOU. Asked by Amor at 2020-03-01 17:32:57
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.
35 I cannot download those files under 'Download' tag. Please reply as soon as possible?THANK YOU. Asked by Rachel at 2020-03-05 21:57:30
Sorry. I can send the data to you. Please contact me (liuzy1984@163.com)
36 I cannot download the ingredient-target-pathway/disease network Asked by Kathy at 2020-03-28 14:52:20
The function works well. You can try another kind of web browser or another computer.
37 How to obtain the all ingredient list of the herb?I can not use the TAMID ID to get this.And if i want to obtain all ingredient of the herb,can i use TCMID directly? Asked by Geng at 2020-04-20 09:31:07
In BATMAN-TCM, ingredient-herb association data indeed are from TCMID. You can use TCMID data directly.
38 In the bioinformatics analyses of potential targets?I have noticed that some of adjusted P-value had been marked in red?What is the meaning? Asked by liu at 2020-08-28 16:35:20
If the P-value<=cutoff you have set, it will be marked in red.
39 PLEASE EXPLAIN HOW TO CALCULATE ENRICH RATIO OF KEGG IN DETAIL, BECAUSE BATMAN SHOWS ENRICH RATIO IS MORE THAN 1,BUT SOME PAPERS SAY IT IS LESS THAN 1,WHY Asked by TAO LIU at 2021-03-29 10:29:01
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.
40 Thank you for your useful database. I have a question: How do I analyze the Bioinformatics of known targets (including DrugBank, KEGG or TTD). This means that it does not include predicted targets. Should I choose a cutoff score of 1000? Asked by Minh at 2021-04-05 21:20:13
I think that "choose a very large score cutoff" is a solution for your need.
41 Thank you for your excellent database. I'd like to how can I Reverse search from gene symbol to herbs' active compounds? Asked by Kong at 2021-08-18 22:59:14
Sorry?this function is not supported by current BATMAN-TCM. In version2.0, this function will be supported.
42 How the compounds of herb were predicted? Would you please explain the selection standard of these compounds? How about the absorption characters and the concentrations in vivo? Thank you! Asked by Rui at 2021-09-17 14:48:59
Our prediction of traditional Chinese medicine targets is obtained through similarity algorithms?based on known drug-target data from DrugBank. You can learn all the details in our paper?PMC4754750?. As for the screening criteria for compounds, our data is sourced from TCMID, an integrated database of Chinese herbal medicine resources widely recognized in the field. Unfortunately, we have not compiled pharmacokinetic data for these compounds. However, this is a valuable suggestion, and we will consider incorporating such data in the future.
43 How can the downloaded herbal medicine target file have no score? It's troublesome to organize the documents Asked by lily at 2021-10-24 16:35:39
I apologize for the inconvenience caused. It may have been due to a network issue that resulted in the incorrect parsing of the returned results. We have rechecked the server's operation status, and I kindly request you to resubmit your analysis. I believe you will receive satisfactory results this time.
44 Provide me a tutorial how to use this platform, as I am a new user? Asked by Prasanth at 2021-12-30 19:09:00
45 Hello, I would like to know, in this herbal list, I input a prescription, and the summary in the target prediction result that appears, the relevant herbs are the herbs I entered, only found so many or just related. Because I found that I entered 20 herbs, and only 8 related herbs appeared. Looking forward to your reply, thank you! Asked by HU at 2022-02-18 13:35:49
This may be due to an incorrect input format. It is recommended to input one Pinyin/Latin/English name per line, with spaces separating the Pinyin names.
46 The medicine cannot be loaded after input Asked by WANGNING at 2022-10-24 21:33:43
I apologize for any inconvenience caused. If you are experiencing network or server issues, please try again later. If the problem persists, please let us know, and we will do our best to resolve it and provide assistance. Thank you for your understanding and patience.
47 Why is the content I see on the site different from the content you download, especially the KEGG channel and net network parts Asked by Xin yiran at 2023-02-15 14:33:20
This may be because we provide downloads for all prediction results, while the website only presents results that meet the Score cutoff and p-value cutoff parameters, along with the analysis of these results.
48 I would like to express my gratitude to the team for developing this platform. However, I'm facing an issue when loading the KEGG pathway graph. Despite waiting for 30 minutes as instructed, I receive an error message. I would greatly appreciate your assistance in resolving this matter. Additionally, I seek your advice on selecting an appropriate score cutoff for different cases. Thank you for your dedication, and I eagerly await your response. Asked by Alena at 2023-07-06 11:14:53
49 why “ Compound list” is not working?progress is 0% all the time Asked by hua at 2023-09-05 15:53:17
50 why my job disappear?even it have not finished. Asked by bu at 2023-09-10 20:24:18
You can fill your email. When the job is finished, you will recieve a notification email.
51 ???????????????????????????????????????? Asked by SHAO at 2024-02-04 22:22:52
52 ?????????????The jobid in the URL you input seems incorrect. Please check and re-input! Asked by joe at 2024-02-09 11:50:44
53 in Parameters setting, there is "Score cutoff " to screening the potential targets. I would like to know how these scores are determined. Asked by NIU at 2024-03-12 22:45:28
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Contact: Zhongyang Liu, liuzy1984@163.com, Beijing Proteome Research Center, Beijing, China.