BioC.dtd

<!-- Combination DTD that will work with any document so far. -->

<!--

    Some believe XML is easily read by humans and that should be
    supported by clearly formatting the elements. In the long run,
    this is destracting. While the only meaningful spaces are in text
    elements and the other spaces can be ignored, current tools add no
    additional space.  Formatters and editors may be used to make the
    XML file appear more readable.

    The possible variety of annotations that one might want to produce
    or use is nearly countless. There is no guarantee that these are
    organized in the nice nested structure required for XML
    elements. Even if they were, it would be nice to more easily
    ignore unwanted annotations.  So annotations are recorded in a
    stand off manner, external to the annotated text. The exceptions
    are passages and sentences because of their fundamental place in
    text.

    The text is expected to be encoded in Unicode, specifically
    utf-8. This is one of the encodings required to be implented by
    XML tools, is portable between big-endian and little-endian
    machines and is a superset of 7-bit ASCII. Code points beyond 127
    may be expressed directly in utf-8 or indirectly using numeric
    entities.  Since many tools today still only directly process
    ASCII characters, conversion should be available and
    standardized.  Offsets should be in 8 bit code units (bytes) for
    easier processing by naive programs.

    Nothing final. Just current thoughts.

    collection:  Group of documents, usually from a larger corpus. If
    a group of documents is from several corpora, use several
    collections.

    source:  Name of the source corpus from which the documents were selected

    date:  Date documents extracted from original source. Can be as
    simple as yyyymmdd or an ISO timestamp.

    key: Separate file describing the types used and any other useful
    information about the data in the file. For example, if a file
    includes part-of-speech tags, this file should describe the
    part-of-speech tags used.

    infon: key-value pairs. Can record essentially arbitrary
    information. "type" will be a particular common key in the major
    sub elements below. For PubMed references, passage "type" might
    signal "title" or "abstract". For annotations, it might indicate
    "noun phrase", "gene", or "disease". In the programming language
    data structures, infons are typically represented as a map from
    strings to strings.  This means keys should be unique within each
    parent element.

    document:  A document in the collection. A single, complete
    stand-alone document as described by it's parent source.

    id:  Typically, the id of the document in the parent
    source. Should at least be unique in the collection.

    passage:  One portion of the document.  For now PubMed documents
    have a title and an abstract. Structured abstracts could have
    additional passages. For a full text document, passages could be
    sections such as Introduction, Materials and Methods, or
    Conclusion. Another option would be paragraphs. Passages impose a
    linear structure on the document. Further structure in the
    document can be implied by the infon["type"] value.

    offset: Where the passage occurs in the parent document. Depending
    on the source corpus, this might be a very relevant number.  They
    should be sequential and identify a passage's position in
    the document.  Since pubmed is extracted from an XML file, the
    title has an offset of zero, while the abstract is assumed to
    begin after the title and one space.

    text: The original text of the passage.

    sentence:  One sentence of the passage.

    offset: A document offset to where the sentence begins in the
    passage. This value is the sum of the passage offset and the local
    offset within the passage.

    text: The original text of the sentence.

    annotation:  Stand-off annotation

    id: Used to refer to this annotation in relations.

    location: Location of the annotated text. Multiple locations
    indicate a multi-span annotation.

    offset: Document offset to where the annotated text begins in
    the passage or sentence. The value is the sum of the passage or
    sentence offset and the local offset within the passage or
    sentence.

    length: Length of the annotated text. While unlikely, this could
    be zero to describe an annotation that belongs between two
    characters.

    text:  Unless something else is defined one would be expect the
    annotated text. The length is redundant in this case. Other uses
    for this text could be the normalized ID for a gene in a gene
    database. 

    relation: Relationship between multiple annotations.

    id: Used to refer to this relation in other relationships.

    refid: Id of an annotated object or other relation.

    role: Describes how the referenced annotated object or other
    relation participates in the current relationship. Has a default
    value so can be left out if there is no meaningful value.

-->

<!ELEMENT collection ( source, date, key, infon*, document+ ) >
<!ELEMENT source (#PCDATA)>
<!ELEMENT date (#PCDATA)>
<!ELEMENT key (#PCDATA)>
<!ELEMENT infon (#PCDATA)>
<!ATTLIST infon key CDATA #REQUIRED >

<!ELEMENT document ( id, infon*, passage+, relation* ) >
<!ELEMENT id (#PCDATA)>

<!ELEMENT passage ( infon*, offset, ( ( text?, annotation* ) | sentence* ), relation* ) >
<!ELEMENT offset (#PCDATA)>
<!ELEMENT text (#PCDATA)>

<!ELEMENT sentence ( infon*, offset, text?, annotation*, relation* ) >

<!ELEMENT annotation ( infon*, location*, text ) >
<!ATTLIST annotation id CDATA #IMPLIED >
<!ELEMENT location EMPTY>
<!ATTLIST location offset CDATA #REQUIRED >
<!ATTLIST location length CDATA #REQUIRED >

<!ELEMENT relation ( infon*, node* ) >
<!ATTLIST relation id CDATA #IMPLIED >
<!ELEMENT node EMPTY>
<!ATTLIST node refid CDATA #REQUIRED >
<!ATTLIST node role CDATA "" >