XML

1. Interexchance Languages
XML
COBRA
UMLS

2. XML
● eXtensible Markup Language
● Used for data exchangeover the web
● Similar to HTML
● Uses document type definition to define data
● Mainly used to make spreadsheets for financial
data
● It allows one to create new tags
●

3. XML
● Stores data with user defined tags
● XML data can be embedded with HTML code
and then used to display within a browser
● Its flexibility and robustness makes it a
excellent choice to share data
● BLAST, FASTA produce XML format results
● NCBI, EMBL, DDBJ all use XML format
● PIR database can be downloaded in XML
● Also the Gene Ontology data

4. XML Example
<?XML> version=”1.0”?>
<eSearchResult>
<Count>39655</Count>
<RetMax>10</Retmax>
<RetStart>0</RetStart>
<IdList Date=”14/03/2015”>
<IdList>123456789</ID>
<IdList>123456799</ID>
<IdList>123456999</ID>
<IdList>123459999</ID>
</IdList>
</eSearchResult>

5. ●
1st
line – XML Declaration – declares version
●
2nd
line – first element of the root of document
<eSearchResult>
an object resulting from Entrex search
● Next 4 lines – child elements
IdList, Count, RetMax, RetStart
● IdList has a date attribute and multiple Id
sublements

6. NOTE
● All tags are case sensitive
● All elements must have a matching closing tag
● All elements must be correctly nested
● All attribute values must be quoted (“abc”)

7. Output
● EsearchResult
– Count
– RetMax
– RetStart
– IdList
● ID
● ID
● ID
● ID
123456789
123456799
123456999
123459999