Biomedical books by Jules J. Berman, Ph.D., M.D.


biomedical informatics cover Perl Programming for Medicine and Biology Cover Neoplasms: Principles of Development and Diversity, by Jules J. Berman, cover Ruby for Medicine and Biology Cover



















Taxonomy look-up

If you have trouble thinking of an organism to enter in the query box (above), here are some suggestions:
                      
Actinomyces                Lemur
Alligator                  Maple trees          
Apple                      Mycobacterium        
Balantidium coli           Necator americanus   
Banana                     Oats                 
Brevoortia                 Oysters
Cancer pagurus             Pea                  
Candida albicans           Plasmodium vivax     
Canis                      Rattus rattus        
Cashew                     Sugar maple          
Chigger                    Spiders    
Chicken                    Taenia solium        
Coccidioides immitis       Toxoplasma gondii    
Cocoa                      Trichomonas          
Corn                       Turkey               
Danio rerio                Ursus                
Escherichia coli           Vibrio cholera              
Harvestmen                 Wheat                  
Helicobacter pylori        Zebrafish        
Kangaroo                 

Phylogeny is the ancestral lineage for an organism, begining at the species level and descending to the primordial organism from which all extant species evolved.

For example, the lineage for Homo sapiens is:
Homo sapiens
Homo
Homo/Pan/Gorilla group
Hominidae
Hominoidea
Catarrhini
Simiiformes
Haplorrhini
Primates
Euarchontoglires
Eutheria
Theria
Mammalia
Amniota
Tetrapoda
Sarcopterygii
Euteleostomi
Teleostomi
Gnathostomata
Vertebrata
Craniata
Chordata
Deuterostomia
Coelomata
Bilateria
Eumetazoa
Metazoa
Fungi/Metazoa group
Eukaryota
cellular organisms

An excellent, public source of information on organismal phylogeny is taxonomy.dat a 100+ Mbyte file available from the European Bioinformatics Institute.

The taxonomy.dat file lists over 400,000 species, as a taxonomy (i.e., assigning a parent class to every specie), providing a species id number and an id number for the parent class.

Using this information, it is possible to compute the complete classification hierarchy for each of the 400 hundred thousand plus named organism in taxonomy.dat

By entering the full name of any organism (included in taxonomy.dat) in the input box, and pressing the submit button, you will get the taxonomic entry for the organism, followed by its phylogenetic hierarchy.
Last modified: August 23, 2008

Biomedical Informatics, by Jules J. Berman, cover Ruby: The Programming Language, by Jules J. Berman, cover Perl: The Programming Language, by Jules J. Berman, cover


















Perl Programming for Medicine and Biology, by Jules J. Berman, cover Neoplasms: Principles of Development and Diversity, by Jules J. Berman, cover Ruby for Medicine and Biology, by Jules J. Berman, cover