The Entry Structure

The entire database Sample/SH2 is stored in Darwin as a string of length DB[TotEntries]. Figure  gives a graphical view of how information is organized internally. DB[string] points to the beginning of this name. Recall that each entry from a sequence database in Darwin is wrapped in the SGML tags <E>, </E>. To extract the entire contents of an entry, we use the Entry structured type.

> ReadDb('Sample/SH2');
> first := Entry(1);
first := Entry(1)
> second := Entry(2);
second := Entry(2)
> last_three := Entry(76, 77, 78);
last_three := Entry(76,77,78)
> print(first);
<E><ID>ABL1_CAEEL</ID><AC>P03949;</AC><DE>TYROSINE-PROTEIN 
KINASE ABL-1 (EC 2.7.1.112) (FRAGMENT).</DE><OS>CAENORHABD
ITIS ELEGANS.</OS><OC>EUKARYOTA; METAZOA; ACOELOMATES; NEM
ATODA; SECERNENTEA; RHABDITIDA.</OC><KW>TRANSFERASE; TYROS
INE-PROTEIN KINASE; SH2 DOMAIN; SH3 DOMAIN.</KW><FT>ACT_SI
TE 283 283</FT><SEQ>NNEWCEARLYSTRKNDASNQRRLGEIGWVPSNFIAPYN
SLDKYTWYHGKISRSDSEAILGSGITGSFLVRESETSIGQYTISVRHDGRVFHYRINV
DNTEKMFITQEVKFRTLGELVHHHSVHADGLICLLMYPASKKDKGRGLFSLSPNAPDE
WELDRSEIIMHNKLGGGQYGDVYEGYWKRHDCTIAVKALKEDAMPLHEFLAEAAIMKD
LHHKNLVRLLGVCTHEAPFYIITEFMCNGNLLEYLRRTDKSLLPPIILVQMASQIASG
MSYLEARHFIHRDLAARNCLVSEHNIVKIADFGLARFMKEDTYTAHAGAKFPIKWTAP
EGLAFNTFSSKSDVWAFGVLLWEIATYGMAPYPGVELSNVYGLLENGFRMDGPQGCPP
SVYRLMLQCWNWSPSDRPRFRDIHFNLENLISSNSLNDEVQKQLKKNNDKKLESDKRR
SNVRERSDSKSRHSSHHDRDRDRESLHSRNSNPEIPNRSFIRTDDSVSFFNPSTTSKV
TSFRAQGPPFPPPPQQNTKPKLLKSVLNSNARHASEEFERNEQDDVVPLAEKNVR</S
EQ></E>
> print(second);
<E><ID>ABL2_HUMAN</ID><AC>P42684;</AC><DE>TYROSINE-PROTEIN
 KINASE ABL2 (EC 2.7.1.112) (TYROSINE KINASE ARG).</DE><OS
>HOMO SAPIENS (HUMAN).</OS><OC>EUKARYOTA; METAZOA; CHORDAT
A; VERTEBRATA; TETRAPODA; MAMMALIA; EUTHERIA; PRIMATES.</O
C><KW>TRANSFERASE; TYROSINE-PROTEIN KINASE; PROTO-ONCOGENE
; ATP-BINDING; PHOSPHORYLATION; SH2 DOMAIN; SH3 DOMAIN; AL
TERNATIVE SPLICING.</KW><FT>ACT_SITE 409 409</FT><SEQ>MGQQ
VGRVGEAPGLQQPQPRGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHDHFASCVEDG
FEGDKTGGSSPEALHRPYGCDVEPQALNEAIRWSSKENLLGATESDPNLFVALYDFVA
SGDNTLSITKGEKLRVLGYNQNGEWSEVRSKNGQGWVPSNYITPVNSLEKHSWYHGPV
SRSAAEYLLSSLINGSFLVRESESSPGQLSISLRYEGRVYHYRINTTADGKVYVTAES
RFSTLAELVHHHSTVADGLVTTLHYPAPKCNKPTVYGVSPIHDKWEMERTDITMKHKL
GGGQYGEVYVGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCT
LEPPFYIVTEYMPYGNLLDYLRECNREEVTAVVLLYMATQISSAMEYLEKKNFIHRDL
AARNCLVGENHVVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNTFSIKSDV
WAFGVLLWEIATYGMSPYPGIDLSQVYDLLEKGYRMEQPEGCPPKVYELMRACWKWSP
ADRPSFAETHQAFETMFHDSSISEEVAEELGRAASSSSVVPYLPRLPILPSKTRTLKK
QVENKENIEGAQDATENSASSLAPGFIRGAQASSGSPALPRKQRDKSPSSLLEDAKET
CFTRDRKGGFFSSFMKKRNAPTPPKRSSSFREMENQPHKKYELTGNFSSVASLQHADG
FSFTPAQQEANLVPPKCYGGSFAQRNLCNDDGGGGGGSGTAGGGWSGITGFFTPRLIK
KTLGLRAGKPTASDDTSKPFPRSNSTSSMSSGLPEQDRMAMTLPRNCQRSKLQLERTV
STSSQPEENVDRANDMLPKKSEESAAPSRERPKAKLLPRGATALPLRTPSGDLAITEK
DPPGVGVAGVAAAPKGKEKNGGARLGMAGVPEDGEQPGWPSPAKAAPVLPTTHNHKVP
VLISPTLKHTPADVQLIGTDSQGNKFKLLSEHQVTSSGDKDRPRRVKPKCAPPPPPVM
RLLQHPSICSDPTEEPTALTAGQSTSETQEGGKKAALGAVPISGKAGRPVMPPPQVPL
PTSSISPAKMANGTAGTKVALRKTKQAAEKISADKISKEALLECADLLSSALTEPVPN
SQLVDTGHQLLDYCSGYVDCIPQTRNKFAFREAVSKLELSLQELQVSSAAAGVPGTNP
VLNNLLSCVQEISDVVQR</SEQ></E>
> print(last_three);
E><ID>YRK_CHICK</ID><AC>Q02977;</AC><DE>PROTO-ONCOGENE TYR
OSINE-PROTEIN KINASE YRK (EC 2.7.1.112) (P60-YRK) (YES REL
ATED KINASE).</DE><OS>GALLUS GALLUS (CHICKEN).</OS><OC>EUK
...
E><ID>ZA70_HUMAN</ID><AC>P43403;</AC><DE>TYROSINE-PROTEIN 
KINASE ZAP-70 (EC 2.7.1.112) (70 KD ZETA-ASSOCIATED PROTEI
N).</DE><OS>HOMO SAPIENS (HUMAN).</OS><OC>EUKARYOTA; METAZ
...

<E><ID>ZA70_MOUSE</ID><AC>P43404;</AC><DE>TYROSINE-PROTEIN
 KINASE ZAP-70 (EC 2.7.1.112) (70 KD ZETA-ASSOCIATED PROTE
IN).</DE><OS>MUS MUSCULUS (MOUSE).</OS><OC>EUKARYOTA; META
...

We can isolate the contents of a specific SGML tag by including the tag in single quotes and square brackets.

> first['ID'];     # get the identification tag of the 1st entry
ABL1_CAEEL
> first['SEQ'];    # get the sequence for the 1st entry
NNEWCEARLYSTRKNDASNQRRLGEIGWVPSNFIAPYNSLDKYTWYHGKI
..(557).. DVVPLAEKNVR 

> second['FT'];
ACT_SITE 409 409

> last_three['DE'];         # get the description tag 
                          #for the last three entries
[PROTO-ONCOGENE TYROSINE-PROTEIN KINASE YRK (EC 2.7.1.112) (P60-YRK) (YES REL\
ATED KINASE)., 
TYROSINE-PROTEIN KINASE ZAP-70 (EC 2.7.1.112) (70 KD ZETA-ASSOCIATED PROTEIN)., 
TYROSINE-PROTEIN KINASE ZAP-70 (EC 2.7.1.112) (70 KD ZETA-ASSOCIATED PROTEIN).]

Notice that when an Entry structure has only a single posint parameter, as is the case with first and second above, and we select for a specific tag, then it returns the contents contained in this field as a name object. When more than one entry is specified, as is the case with last_three, it returns a list of string objects. The i^th element of this list corresponds to the i^th parameter of Entry.^8.1

  

Figure: A diagram showing the database structure DB. Here DB is a protein database consisting of 78 sequences from Swiss-Prot. The newline characters have been changed to space symbols.