Pedigree/Draw survey

Bennett Dyke bdyke at DARWIN.SFBR.ORG
Thu Apr 2 15:25:29 EST 1992


                       PEDIGREE/DRAW USERS SURVEY

To any unregistered users of Pedigree/Draw for the Macintosh whom I may 
have missed in my snail-mail survey:

I am in the process of deciding future directions for Pedigree/Draw and 
could use your help.  

1.  As many of you know, we make frequent updates of the program in 
response to suggestions for improvements and reports of bugs.  We have a 
list of changes planned for the future, the most prominent of which are 

*   Precise control of order of sibs (for example, by birth date). 
*   Increase in the number of multiple matings permitted. 
*   Improved handling of larger pedigrees (n>500). 
*   On-screen editing of pedigree diagram (ability to move individuals 
    while maintaining links to relatives). 
*   Tools for importing and exporting data with foreign formats such as 
    LIPED, LINKAGE, dBASE, Lotus, etc. 
*   Display of pedigree data in tabular form. 
*   Features that would allow display of selected subsets of a drawn     
    pedigree. 
*   Capability of displaying pedigrees of self-fertilizing organisms. 
*   More flexible control over text display. 
*   Symbol editing and expansion of symbol palettes . 
*   Full support for installed fonts. 
*   Increased support for importation and display of picture data. 
*   Various general improvements in drawing speed, pedigree layout, etc.

Please give suggestions for other features you would like us to 
incorporate.

The current version of Pedigree/Draw is release 4.3B3, dated Nov/1991.  
Version 4.4 is tentatively planned for release in June/1992, version 5.0 
(a major upgrade) in Sept/1992.

2.  Pedigree/Draw is currently implemented only on the Macintosh.  Would 
it be useful to you if we transferred the package to Unix (X-Windows)?
NOTE:  We will continue to avoid what we see as the insurmountable
problems of adapting our code to MS-DOS, but at some time in the future
we might move Pedigree/Draw to OS/2 or Windows NT.  This will have to
wait until it becomes clear which operating system is the more successful
and popular.

3.  Would it be useful to you if we linked Pedigree/Draw into a full-
scale pedigree database system?  Our system of choice is PEDSYS, a 
package we have developed and have been using over the past ten years in 
the Population Genetics Laboratory at the Southwest Foundation.  PEDSYS 
is described briefly below.  The general idea would be (a) to supplement 
conventional text-based reporting functions (listings, tables, etc.) with 
genealogical diagrams, where appropriate, and (b) to make it possible to 
point to an individual displayed on the screen in an extended pedigree 
diagram, and have textual information for that individual appear in a 
window, print file, etc.  Please indicate whether or not this would be 
of use to you.

4.  Would you also tell me if you use Pedigree/Draw frequently, 
occasionally or never.

5.  What database system are you using to keep your pedigree data?

Many thanks in advance for your replies.

                                 PEDSYS

PEDSYS is a database system developed as a specialized tool for 
management of genetic and pedigree data.  The system supports the 
collection, management and analysis of constantly evolving data sets by 
investigators in several different laboratories.  It is not dependent on 
any one type of computer or operating system.  Currently it is 
implemented in Sun Microsystems Unix, MS-DOS and Macintosh OS, and can 
readily exchange data with other database systems, programs and 
computers.  Particular care has been taken to make it possible for non-
experts to use PEDSYS effectively without extensive training, but at the 
same time to avoid irritating the proficient user.

Functions:

GENERAL DATA MANAGEMENT    
 1. AGE      Calculates age in years, months, or days   
 2. BROWSE   Gives formatted screen display of any file   
 3. CALC     Generates functions of one or more items  
 4. DATES    Converts between a variety of calendar date formats  
 5. DUPLIC   Identifies records with duplicate item values  
 6. LIST     Lists contents of Master or Data File on printer 
 7. MERGE    Merges records from one file with records of another file
 8. REFORMAT Reorders, deletes, or reformats items of records in file
 9. REPLACE  Replaces item entries as specified by a substitution table
10. REPORT   Lists Multiple-entry records of individuals on printer 
11. SHOW     Displays Single-entry records of EGO, FA and MO 
12. SHOWDATA Displays Multiple-entry records of a single individual 
13. SORT     Performs compound sort of records in file 
14. SUBSET   Generates compound subsets of records in file 
15. TALLY    Generates distributions and calculates means and variances

PEDIGREE MANAGEMENT

 1. ANCESTOR Finds common ancestors for selected probands 
 2. COUNTPED Identifies pedigrees and assigns individuals to them 
 3. EXCLUDE  Identifies parental exclusions and probabilities of 
             paternity 
 4. FASTKIN  Calculates inbreeding, kinship coefficients (Quaas-
             Henderson) 
 5. FOUNDREP Determines founder representation in subsequent generations
 6. GENCHECK Checks marker phenotypes for consistency with Mendelian 
             laws 
 7. GENEFREQ Calculates gene and genotype frequencies from phenotypic 
             data 
 8. GENEDROP Simulates Mendelian segregation in pedigrees 
 9. INFER    Infers unknown genotypes from genotypes of relatives 
10. KINSHIP  Calculates inbreeding, kinship coefficients (Stevens-Boyce)
11. MAKEPED  Constructs extended pedigrees for specified probands 
12. NUCFAM   Groups selected items for FA, MO and offspring 
13. PEDCHECK Tests consistency of gender and dates in nuclear families
14. SEGREGAT Tallies offspring genotypes by parental mating type

FILE MANAGEMENT

 1. ALTERDAT Updates Data Files (edit, add records, start new file) 
 2. ALTMASTR Creates Master File update file (edit, add records, etc.) 
 3. APPEND   Joins two files having the same Code File specifications 
 4. CODE     Generates a format Code File 
 5. COMBINE  Assembles Multiple-entry values into single records 
 6. DATALINK Links Data Files to Master Files (and internally as needed) 
 7. DBFILER  Adds, edits, removes Master and Data Files in DBFILES 
 8. DELRECS  Deletes records using output of ALTERDAT, ALTMASTR, 
             IMPORTER 
 9. IMPORTER Converts foreign ASCII data records to PEDSYS format 
10. INDEX    Transforms pedigree data into Master File format 
11. ITEMIZE  Determines PEDSYS format of foreign ASCII data records 
12. SETDATA  Updates Data Files using output from ALTERDAT or IMPORTER
13. SETMASTR Updates Master Files using output from ALTMASTR or IMPORTER
14. TRANSLAT Converts between PEDSYS format and character-delimited 
             fields 
15. VERIFIER Checks record format against Code File specifications

Technical:

The database has a partially relational structure that incorporates 
three sets of pointers:

PEDSYS databases are organized around a Master File containing basic 
information on vital events and genealogical relationships for 
individuals in the population.  Master File records incorporate (as 
data) a set of pointers that link each individual with key members of 
the nuclear family.  Thus, the Master File carries its own indexing for 
family members, making it possible to construct extended families 
without the need to access additional files.  A separate index file 
relates these pointers to Permanent IDs of individuals.

Any number of independently developed Data Files can be joined as needed 
to the appropriate Master File by means of a multiple data pointer file 
containing pointers that relate records in the two files.  Data Files 
can be copied or combined in various ways to form entirely new files 
that maintain their linkage with the Master File.

A specialized Multiple Entry Data File, which (unlike other PEDSYS 
files) may contain more than one record for each individual, is used to 
ensure efficient storage of data that may be measured repeatedly on the 
same individual.  Each record in these files contains a pointer that 
links it to other records for the same individual in the file.

This arrangement of files makes it possible for investigators and 
technical staff to manage and analyze data generated in their own 
projects, and at the same time to combine these data (a) with a common 
pool of demographic and genealogical information about the population 
and (b) with data sets collected in other projects.

Data files contain formatted records containing nothing but data 
represented by printable ASCII characters.


-- 
+----------------------------------------------------------------------------+
|   Bennett Dyke                                                             |
|   Department of Genetics               Internet:  bdyke at darwin.sfbr.org    |
|   Southwest Foundation                    Phone:  (512) 674-1410 Ext 281



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