  The paper describes the ALVIS annotation format designed for the indexing of
large collections of documents in topic-specific search engines. This paper is
exemplified on the biological domain and on MedLine abstracts, as developing a
specialized search engine for biologists is one of the ALVIS case studies. The
ALVIS principle for linguistic annotations is based on existing works and
standard propositions. We made the choice of stand-off annotations rather than
inserted mark-up. Annotations are encoded as XML elements which form the
linguistic subsection of the document record.
