Contents of a BMRB standard compound(s) deposition
- A description of the chemical compound(s) studied (PubChem CID or SID or molecular structure file - .mol file or .sdf file)
- The source of the compound(s) (vendor)
- Contents of the samples used
- Sample conditions used
- A description of the NMR spectrometer(s) used
- Names of the people that collected the data and are making the deposition
And at least one or more of the following:
- Time-domain NMR data collected including acquisition parameter files
- Peak lists from each of the NMR spectra collected
- Assigned chemical shifts for the compound(s)
Creating a BMRB standard compound(s) deposition
- Complete a deposition form for each compound included in your data upload. Here is an example of a completed form and a metabolomics deposition specifications document in MS word format.
- 'tar' all of the files in your data upload together and compress the tar file using zip or gzip
- Use anonymous ftp to upload the data.
- Send an email to firstname.lastname@example.org that contains the name of the uploaded file
Since the data sets can become quite large, we ask that you archive your files with the tar utility and then compress them with zip or gzip. Refer to your operating system's instructions for more information about tar, zip, and gzip.
Submitting a deposition to BMRB
To deposit time-domain data, you need to use the File Transfer Protocol (FTP). Since a web browser tends to limit the size of the files that can be transfered through FTP, we suggest that you do not use your browser to transfer time-domain data sets. There are software packages for using FTP, but if you are using a Windows, UNIX, Linux, or Mac OSX computer, FTP is a built in function of its command line interface.
If you have more than five files, please collate them into one large file using tar, the text archiving format software. After your data has been collated, it should also be compressed, preferably with zip or gzip.
If you are using software with a graphical user interface, follow the instructions that accompany it.
If you are using the command line interface, the first thing you need to do is navigate to the directory that contains the information you want to upload. Use the command 'cd' on UNIX and UNIX-like operating systms, and use the command 'CHDIR' on Windows. If you are not familiar with this, someone in your group probably is.
Next, connect to the BMRB FTP server by typing:
system prompt$ftp ftp.bmrb.wisc.edu
You should get a message that says
Connected to ftp.bmrb.wisc.edu (your network address). 220 BMRB FTP server ready Name (ftp.bmrb.wisc.edu:cfschulte):
At the name prompt, enter anonymous and press Enter.
Name (ftp.bmrb.wisc.edu:your login): anonymous
You should get a message that says the login was ok, and a request for an email address or a password. Because you are logging in anonymously, enter your email address.
Name (ftp.bmrb.wisc.edu:cfschulte): anonymous 331 Anonymous login ok, send your complete email address as your password. Password: email@example.com
You should now see an 'ftp' prompt.
If you are transfering a zipped or gzipped file, there is one more thing you must do at this point: set ftp to binary mode by typing 'binary'.
Don't bother doing this, however, if you are sending plain text.
FTP navigation works the same way as navigation on UNIX. Use the command 'cd' (change directory) to move among directories, and ls (list) to view the contents of a directory. Typing 'cd subdirectory will move your position (present working directory, or pwd) to that directory. Typing 'cd ..' will move it to the directory containing your current position. Typing 'pwd' will tell you what your current position is. For a list of commands, type 'help'.
Navigate to the proper directory by typing, 'cd incoming/metabolomics'.
All that is left to do is to upload your data files. Create a new subdirectory, and give it a name that will be obvious that it belongs to your deposition (include your name or the name of your organization and the date). Move (cd) to that directory and upload the data. Use the 'put' command, if you only have one file, otherwise use 'mput' to upload all of your files.
ftp>mkdir jane_doe_20070612 ftp>cd jane_doe_20070612 ftp>mput file1.tar file2.tar.gz etc.str
You're done! Type quit, and you are no longer using FTP.
If your data upload failed, first try repeating the steps above. If you have gone through all of these steps, and are confident that everything was carried out correctly, but have not been able to upload your data, contact firstname.lastname@example.org.