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