From usenet.ucs.indiana.edu!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!cs.utexas.edu!uunet!bionet!WELCHGATE.WELCH.JHU.EDU!kab Fri Jul 17 15:39:04 EST 1992 Article: 4 of bionet.molbio.gdb Path: usenet.ucs.indiana.edu!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!cs.utexas.edu!uunet!bionet!WELCHGATE.WELCH.JHU.EDU!kab From: kab@WELCHGATE.WELCH.JHU.EDU (Kerryn Brandt) Newsgroups: bionet.molbio.gdb Subject: Anonymous FTP access to GDB(TM) and OMIM(TM) files Message-ID: <9207171754.AA08409@welchgate.welch.jhu.edu> Date: 17 Jul 92 17:54:04 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 732 Accessing GDB Files via Anonymous FTP: JUNE 22, 1992 =========================================================================== WHAT IS ANONYMOUS FTP? ---------------------- The GDB Human Genome Data Base at the Johns Hopkins University in Baltimore MD provides Anonymous FTP access to files related to GDB(TM) and OMIM(TM). The types of files include: database statistics, documentation, data, and electronic forms. Other types of information will be added in the future. This service enables users to login to our remote general access computer, mendel.welch.jhu.edu, using a public login/password and to transfer (download) files to their local computer. NOTE: The FTP service is ONLY available to users with Internet access and FTP software on their computers. The service CANNOT be used via BITNET or any other network access. To provide helpful information for both experienced and novice FTP users, this document contains the following sections: . general information . instructions for using FTP . sample FTP session Funding for this project is provided by the U.S. Department of Energy and the U.S. National Institutes of Health. ** G E N E R A L I N F O R M A T I O N ** WHAT YOU NEED TO USE ANONYMOUS FTP ---------------------------------- To use this service, you will need: 1. Software which supports File Transfer Protocol (FTP). 2. Access to Internet. INFORMATION ABOUT THE GENERAL ACCESS COMPUTER, MENDEL ---------------------------------------------------- Name: mendel.welch.jhu.edu IP Address: 128.220.59.42 Data Updates: Data is updated between 9:00 AM and 12 noon Eastern Time every Monday, except holidays. Service may be unavailable during these times. ORGANIZATION AND FORMAT OF AVAILABLE FILES ------------------------------------------ Mendel contains the following directories and subdirectories. A README file in each one describes the content. The file README.ALL in the "top-level" directory includes all the individual README files. gdb related to GDB gdb/data data files gdb/doc user documentation gdb/doc/manual subdirectory with User Manual gdb/register forms for GDB registration gdb/report reports for individual chromosomes gdb/report/cc15 reports for chromosome 15 gdb/schema system documentation gdb/software-update patch files gdb/stats summary of genes and markers per chromosome gdb/submit-data forms for submitting GDB data omim related to OMIM omim/dom MIM documents beginning with "1" (dominant) omim/rec MIM documents beginning with "2" (recessive) omim/xlink MIM documents beginning with "3" (X-linked) omim/distribution OMIM files for Sun version front-end software incoming receive incoming files pub publicly available documents and programs There may also be files in these directories, or additional directories (bin and etc), that are for system use. File names follow these naming conventions: *.asc ASCII format *.ps PostScript format *.tar standard UNIX archive, usually contains multiple smaller files *.Z compressed file format is YYMMDD USING THE GDB AND OMIM DATA FILES --------------------------------- All the GDB and OMIM files are available for downloading only. You cannot do any searching to locate specific data through FTP. The GDB and OMIM databases are available for online searching via Internet or SprintNet. The online GDB database provides output of search results via email. Since output of OMIM search results is currently limited, you can first do your searches in OMIM to identify the MIM numbers for relevant documents and then use those MIM numbers to download the document files from the appropriate OMIM directory. To access these databases on the Welch Library Computer, you must register for a user ID and password. Information and registration forms are in the gdb/register directory. OMIM is also available from a WAIS server, which allows you to both search the database from your computer and download MIM documents. Information about WAIS is in the omim directory in a file called: wais . REVISED VERSION OF THIS GUIDE ----------------------------- When major changes to the FTP service are made, this guide will be updated. The latest version of this document is in the gdb/doc directory in a file called: ftp_guide.asc . ADDITIONAL INFORMATION ABOUT FTP AND INTERNET --------------------------------------------- The book called "Zen and the Art of the Internet: A Beginner's Guide to the internet" by Brendan P. Kehoe, dated January 1992, is available in PostScript form in the pub directory. The file is called: zen_internet_1.0.ps GDB USER SUPPORT ---------------- If you have any questions, problems, or suggestions for improving this guide, please contact GDB User Support by: Internet: help@welch.jhu.edu Phone: (410) 955-7058 Fax: (410) 614-0434 ** I N S T R U C T I O N S F O R U S I N G FTP ** ------------------------------------------------------------------------------- | If you are not familiar with using Anonymous FTP services, this section | | includes the following introductory topics: | | | | . logging into mendel | | . how files are organized on mendel | | . README files | | . using FTP commands | | . how to transfer a file to your local computer | ------------------------------------------------------------------------------- Note that quotation marks and angle brackets < > are used for clarity only: DO NOT TYPE QUOTATION MARKS ! DO NOT TYPE BRACKETS ! LOGGING INTO MENDEL ------------------- To log into the remote mendel computer (128.220.59.42) through Internet: step 1. at your local prompt, type "ftp 128.220.59.42" step 2. at the login(name) prompt, type "anonymous" step 3. at the password prompt, type your email address (this will not display on screen) First you will see a "WELCOME" screen with information about the FTP service and then the FTP prompt: 230 Guest login ok, access restrictions apply. ftp> You will notice that lines displayed by the computer, except the "ftp>" prompt and a few others, are numbered. If your login is not successful, you will see a message indicating "Login incorrect" instead of the "WELCOME" screen. To start the login process again, enter "user anonymous" at the prompt. 530 Login incorrect. Login failed. ftp> user anonymous HOW FILES ARE ORGANIZED ON MENDEL --------------------------------- Files are organized into a hierarchy of directories and subdirectories. In the following diagram which illustrates PART of the hierarchy: . the "top-level" directory is where you are when you login, . there are two subdirectories (gdb, omim), . the "gdb" directory contains three subdirectories (data, doc, stats). "top-level" ---------------------------------------------- | | | | gdb omim ------------------------ | | | | data doc stats To specify the precise "path" from your current location to a subdirectory, use the forward slash "/" to separate the names of the directories. Example: If you have just logged in, the path from the "top-level" directory to the "stats" directory is: gdb/stats README FILES ------------ Each directory and subdirectory contains a file called README, which describes the content of that directory and includes other useful information. When the content of a directory is changed significantly, its README file is also updated. The following example is the README file for the gdb/stats/ directory. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CONTENTS OF gdb/stats DIRECTORY (March 23, 1992) Two types of statistics are generated weekly and added to this directory. 1. These files contains summary statistics showing the total number of genes and markers which have been mapped to each chromosome as of a specific date. loci_chr..asc the format for date is YYMMDD 2. These files contain summary statistics showing the total numbers of GDB objects (loci, probes, polymorphisms, sources, contacts) as of a specific date. gdb_obj..asc the format for date is YYMMDD - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - There is also a file called README.ALL in the "top-level" directory which includes the current version of all the individual README files. If you want information about files from several different directories, it is easier to download the README.ALL file than to download several individual ones. USING FTP COMMANDS ------------------ The following is a list of the basic commands which may be used at the "ftp>" prompt: Command: Result: ------- ------ ls see a list of files and directories dir see a list of files and directories includes information indicating directories, dates, and relative file size cd change directory to cd .. change to directory above current directory pwd see name of current directory get transfer (download) a file to your local computer put transfer (upload) a file from your local computer mget / mput transfer multiple files binary set transfer mode to binary for non-text files ascii set transfer mode to ascii for text files (default) C interrupt file transfer quit exit ftp The asterisk wildcard (*) matches zero or any number of characters and can be used with the "ls", "dir", and "mget" commands to specify a filename pattern. Be sure to pay attention to case. All commands and most filenames are in lower case. NOTE THAT THERE IS NO COMMAND TO DISPLAY A FILE USING FTP. YOU MUST TRANSFER ALL FILES, INCLUDING THE "README" FILES, TO YOUR LOCAL COMPUTER TO SEE THEM. Examples of using some of these commands are included in the section SAMPLE FTP SESSION at the end of this document. HOW TO TRANSFER A FILE ---------------------- To transfer a file from the remote computer mendel to your local computer, you must be in the directory containing the file. Unless you are transferring a file from the "top-level" directory, the first thing to do is change to the appropriate directory. Changing directories -------------------- In this example of transferring files, you are interested in files about GDB statistics. To change to the gdb/stats directory from the "top-level", use the "cd" command and specify the new directory. ftp> cd gdb/stats 250-Please read the file README 250- it was last modified on Thu Feb 27 17:13:40 1992 - 18 days ago 250 CWD command successful. ftp> To see a list of the files in the new directory, use the "ls" command. ftp> ls 200 PORT command successful. 150 Opening ASCII mode data connection for file list. README loci_chr.920313.asc gdb_obj.920403.asc loci_chr.920327.asc . . Saving a list of files in a mendel directory to your local computer ------------------------------------------------------------------- In addition to seeing the list of files displayed on your screen, you can also save the results of the "ls" or "dir" commands in a another file which is automatically transferred to your local computer. To save the listing, use the "ls" or "dir" command and specify the name of the file you want to be transferred to your computer. ftp> ls * lists all files ftp> ls g* lists all files beginning with "g" You will not see the listing displayed, but when you quit your FTP session the file will be on your computer. This is very useful for directories which contain so many files that the listing will scroll off your screen. ASCII vs. binary mode for transferring files -------------------------------------------- There are two modes for transferring files: ascii mode for transfer of text files, example include *.asc and *.ps files CANNOT be used for non-text files binary mode for transfer of non-text files, examples include *.tar and *.Z files CAN be used for text files When you login into the remote computer mendel, the default is ascii transfer mode. If you are sure that the files you are downloading are text files, you do not need to change modes. If you are downloading a non-text file, you MUST CHANGE TO BINARY MODE. At the prompt, type "binary". ftp> binary 200 Type set to I. (for Image) ftp> Binary transfer mode will be in effect until you quit the current FTP session or type "ascii" to change back to ascii mode transfer. Since text files can be successfully transferred in binary mode, but non-text files cannot be transferred in ascii mode, if you are not sure about the type of file you are transferring, it is safest to change to binary mode. Transferring a single file -------------------------- To transfer (download) any file to your local computer, use the "get" command and specify the name of the file as listed on mendel. ftp> get The file on your local computer will have the same name as on the remote computer mendel. Transferring and renaming a single file --------------------------------------- If you want the file on your local computer to have a different name than on the remote computer mendel, use the "get" command and specify a new name after the mendel name. ftp> get This is important if you are transferring README files. Since these files all have the same name, once you have a file named README on your computer, transferring another one with the same name will overwrite the first one. To avoid transferring multiple README files by renaming them, you can transfer the single file README.ALL, which is located in the "top-level" directory and contains all the README files. You may also need to specify a new filename if the mendel filename contains more characters than your local computer allows. Transferring multiple files --------------------------- To transfer several files, use the "mget" command. The asterisk wildcard (*) matches zero or any number of characters and is used to specify a filename pattern. ftp> mget * gets all files ftp> mget loci* gets all files beginning with "loci" You will be prompted to confirm transfer of each file. If you want to transfer many files without confirming each one, you can turn the prompt off by typing "prompt" before typing the mget command. ftp> prompt Interactive mode off. ftp> Typing "prompt" again will turn the prompting back on. The speed of file transfer varies with the amount of network traffic, which is heaviest during the day. Therefore, it is best to download files during non-business hours. ** S A M P L E FTP S E S S I O N ** In the following sample FTP session, you will get: a) the GDB statistics for April 1992 b) the OMIM document for MIM Number 219700 (Cystic Fibrosis) Logging into mendel ------------------- At your local prompt, type: ftp 128.220.59.42 Connected to 128.220.59.42 220 mendel.welch.jhu.edu FTP server (Version 6.13 Thu Dec 12 13:59:00 EST 1991) ready. Name (128.220.59.42): anonymous 331 Guest login ok, send e-mail address as password. Password: 230- WELCOME TO THE GENERAL ACCESS COMPUTER, MENDEL 230- providing FTP service for GDB 230- 230- All files available for FTP are provided by the GDB Human Genome Data 230- Base at The Johns Hopkins University in Baltimore. Files related to 230- GDB(TM) are located in the gdb directory. Files related to OMIM(TM) 230- are located in the omim directory. 230- 230- Each directory includes a README file describing its contents. The 230- README file in this directory contains information about update 230- schedules and guidelines for using the data. The file README.ALL 230- includes all the individual README files. 230- 230- Please report problems to help@welch.jhu.edu or call GDB User Support 230- at (410)955-7058. If you do have problems, try using a dash (-) as the 230- first character of your password -- this will turn off the continuation 230- messages that may be confusing your ftp client. 230- 230- 230-Please read the file README 230- it was last modified on Fri Jun 19 10:00:42 1992 - 3 days ago 230-Please read the file README.ALL 230- it was last modified on Mon Jun 22 13:15:08 1992 - 0 days ago 230 Guest login ok, access restrictions apply. ftp> NOTE: You have successfully logged into mendel and are in the "top-level" directory ready to type commands at the "ftp>" prompt. When you log in or change to a new directory, you will see a message about the README files in the current directory. Remember, you must download the README file to your local computer to read it. Listing files and directories ----------------------------- There are 2 commands (ls, dir) for listing the contents of a directory. If you type just the commands, you will see the contents of the current directory. ftp> ls 200 PORT command successful. 150 Opening ASCII mode data connection for file list. bin etc pub gdb incoming README.ALL README omim 226 Transfer complete. 56 bytes received in 0.037 seconds (1.5 Kbytes/s) ftp> NOTE: "ls" displays only the names and does not distinguish between files and directories. The names are not listed in any specific order. ftp> dir 200 PORT command successful. 150 Opening ASCII mode data connection for /bin/ls. total 37 -rw-r--r-- 1 root daemon 5066 Jun 19 14:00 README -rw-r--r-- 1 root daemon 26047 Jun 22 17:15 README.ALL dr-xr-xr-x 2 root wheel 512 Feb 7 15:23 bin dr-xr-xr-x 3 root wheel 512 Jan 28 16:27 etc dr-xr-xr-x 11 root wheel 512 Jun 19 14:37 gdb drwxrwxrwx 2 root daemon 1024 Jun 19 14:46 incoming drwxr-xr-x 6 root daemon 512 Jun 22 16:59 omim dr-xr-xr-x 2 root daemon 512 Jun 19 14:46 pub 226 Transfer complete. 498 bytes received in 0.13 seconds (3.6 Kbytes/s) ftp> NOTE: The directory names have "d" as first character at the left side of line. The number to the left of the modification date indicates file size. For example, you can see that README.ALL (26047) is a larger file than README (5066). Downloading a large file takes longer than a small file. The names are listed in alphabetical order, with all names in upper case at the beginning of the list. Listing content of gdb directory -------------------------------- To list the contents of a directory further down the hierarchy, include the directory name after the command. ftp> dir gdb 200 PORT command successful. 150 Opening ASCII mode data connection for /bin/ls. total 65 -rw-r--r-- 1 root daemon 40519 Jun 19 14:50 Index -rw-r--r-- 1 root daemon 890 Jun 19 14:21 README dr-xr-xr-x 2 ftp wheel 15872 Jun 22 15:04 data dr-xr-xr-x 3 root daemon 512 Jun 19 14:25 doc drwxr-xr-x 2 root daemon 512 Feb 28 15:14 map.manager dr-xr-xr-x 2 root daemon 512 Jan 28 22:56 register dr-xr-xr-x 3 root daemon 512 Jun 19 14:39 report dr-xr-xr-x 2 root daemon 512 Jan 29 22:35 schema dr-xr-xr-x 2 root daemon 512 Jun 12 17:08 software-update drwxrwxr-x 2 root 218 1024 Jun 20 02:55 stats dr-xr-xr-x 2 root daemon 1024 Jan 29 22:21 submit-data 226 Transfer complete. remote: gdb 706 bytes received in 0.21 seconds (3.3 Kbytes/s) ftp> NOTE: There is a directory called "stats". Listing contents of gdb/stats directory --------------------------------------- To verify that the statistics files are in the "stats" directory, list its contents. ftp> ls gdb/stats 200 PORT command successful. 150 Opening ASCII mode data connection for file list. gdb/stats/README gdb/stats/loci_chr.920313.asc gdb/stats/gdb_obj.920403.asc gdb/stats/loci_chr.920327.asc gdb/stats/gdb_obj.920327.asc gdb/stats/loci_chr.920228.asc gdb/stats/loci_chr.920306.asc gdb/stats/loci_chr.920320.asc gdb/stats/gdb_obj.920320.asc gdb/stats/loci_chr.920403.asc gdb/stats/gdb_obj.920410.asc gdb/stats/loci_chr.920410.asc gdb/stats/gdb_obj.920417.asc gdb/stats/loci_chr.920417.asc gdb/stats/gdb_obj.920424.asc gdb/stats/loci_chr.920424.asc 226 Transfer complete. remote: gdb/stats 113 bytes received in 0.0061 seconds (18 Kbytes/s) ftp> NOTE: The format for date is YYMMDD, so the statistics files for April 1992 are the 8 files with "9204" in their filename. To download these files, you must be in the gdb/stats directory. Changing to gdb/stats directory -------------------------------- ftp> cd gdb/stats 250-Please read the file README 250- it was last modified on Mon Mar 23 17:12:09 1992 - 91 days ago 250 CWD command successful. ftp> Checking which directory you are in ----------------------------------- ftp> pwd 257 "/gdb/stats" is current directory. ftp> Transferring the statistics files for April 1992 to your local computer ----------------------------------------------------------------------- Since you want to get several files, use the "mget" command with the filename pattern. In this example, the files on your computer will have the same filename as on mendel. ftp> mget *9204* mget gdb_obj.920403.asc? y 200 PORT command successful. 150 Opening ASCII mode data connection for gdb_obj.920403.asc (604 bytes). 226 Transfer complete. local: gdb_obj.920403.asc remote: gdb_obj.920403.asc 639 bytes received in 0.0092 seconds (68 Kbytes/s) mget gdb_obj.920410.asc? . . ftp> NOTE: You will be prompted to confirm transfer of each file that matches the filename pattern. Type "y" or "n". The files are presented in alphabetical order. The line- local: gdb_obj.920403.asc remote: gdb_obj.920403.asc shows the files involved in the transfer process. "local" refers to your local computer, "remote" refers to mendel. As you can see, your local file will have the same name as the file on mendel. Changing to "top-level" directory --------------------------------- If you want to now get an OMIM document, you must first backup 2 levels to the "top-level" directory where you were when you first logged in. It is helpful to use the "pwd" command to check your current directory each time you change to a new directory. ftp> pwd 257 "/gdb/stats" is current directory. ftp> cd .. 250-Please read the file README 250- it was last modified on Fri Jun 19 10:21:03 1992 - 3 days ago 250 CWD command successful. ftp> pwd 257 "/gdb" is current directory. ftp> cd .. 250 CWD command successful. ftp> pwd 257 "/" is current directory. ftp> NOTE: The "/" indicates you are at the "top-level" directory. Changing to omim directory -------------------------- ftp> cd omim 250-Please read the file README 250- it was last modified on Mon Jun 22 13:15:42 1992 - 0 days ago 250 CWD command successful. ftp> ftp> pwd 257 "/omim" is current directory. Listing contents of omim directory ---------------------------------- ftp> dir 200 PORT command successful. 150 Opening ASCII mode data connection for /bin/ls. total 10761 -rwx------ 1 root daemon 24576 Feb 6 15:28 Omim.exe -rw-r--r-- 1 root daemon 1761 Jun 22 17:15 README drwxr-xr-x 2 root daemon 512 Jun 22 13:33 distribution drwxr-xr-x 2 root daemon 60928 Jun 22 13:30 dom -rw-r--r-- 1 root daemon 330314 Jun 22 13:23 dom.index -rw-r--r-- 1 root daemon 2382281 Jun 10 13:04 master.dom.part1.tar.Z -rw-r--r-- 1 root daemon 1977770 Jun 10 13:06 master.dom.part2.tar.Z -rw-r--r-- 1 root daemon 1735731 Jun 10 13:07 master.dom.part3.tar.Z -rw-r--r-- 1 root daemon 1853985 Jun 10 13:10 master.rec.part1.tar.Z -rw-r--r-- 1 root daemon 1268951 Jun 10 13:11 master.rec.part2.tar.Z -rw-r--r-- 1 root daemon 1041307 Jun 10 13:12 master.xlink.tar.Z drwxr-xr-x 2 root daemon 26624 Jun 22 13:31 rec -rw-r--r-- 1 root daemon 170331 Jun 22 13:23 rec.index -rw-r--r-- 1 root daemon 4370 Jun 19 14:15 wais drwxr-xr-x 2 root daemon 6144 Jun 22 13:32 xlink -rw-r--r-- 1 root daemon 37499 Jun 22 13:23 xlink.index 226 Transfer complete. 1107 bytes received in 0.35 seconds (3.1 Kbytes/s) ftp> NOTE: The directory containing MIM documents (dom, rec, xlink) are indicated with a "d" at the left side of the line. Differences in file size can be easily seen by comparing "dom.index" (330314) and "README" (1761). Transferring and renaming the README file ----------------------------------------- Transfer the README file so it is named "readme_omim" on your local computer. ftp> get README readme_omim 200 PORT command successful. 150 Opening ASCII mode data connection for README (1772 bytes). 226 Transfer complete. local: readme_omim remote: README 1820 bytes received in 0.017 seconds (1.1e+02 Kbytes/s) ftp> NOTE: The line- local: readme_omim remote: README shows the files involved in the transfer process. "local" refers to your local computer, "remote" refers to mendel. As you can see, your local file will have a different name. Changing to "rec" directory -------------------------- Since the MIM Number 219700 document begins with "2", it will be in the "rec" directory. ftp> cd rec 250 CWD command successful. ftp> pwd 257 "/omim/rec" is current directory. ftp> Transferring a MIM document -------------------------- Transfer the file named "219700" so it is called "cf_omim" on your local computer. ftp> get 219700 cf_omim 200 PORT command successful. 150 Opening ASCII mode data connection for 219700 (121432 bytes). 226 Transfer complete. local: cf_omim remote: 219700 123549 bytes received in 0.95 seconds (1.3e+02 Kbytes/s) ftp> Exiting FTP ----------- ftp> quit 221 Goodbye. NOTE: You will return to your local computer prompt. BE SURE TO EXIT FTP WHEN YOU ARE DONE. IF YOU DO NOT TYPE ANY COMMAND FOR 15 MINUTES, YOU WILL AUTOMATICALLY BE DISCONNECTED. - END OF DOCUMENT -