simple_bioc 0.0.1
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- checksums.yaml +7 -0
- data/.gitignore +18 -0
- data/Gemfile +4 -0
- data/LICENSE +20 -0
- data/LICENSE.txt +22 -0
- data/README.md +29 -0
- data/Rakefile +8 -0
- data/lib/simple_bioc/annotation.rb +11 -0
- data/lib/simple_bioc/bioc_reader.rb +102 -0
- data/lib/simple_bioc/bioc_writer.rb +93 -0
- data/lib/simple_bioc/collection.rb +15 -0
- data/lib/simple_bioc/document.rb +29 -0
- data/lib/simple_bioc/location.rb +10 -0
- data/lib/simple_bioc/node.rb +12 -0
- data/lib/simple_bioc/node_base.rb +14 -0
- data/lib/simple_bioc/passage.rb +29 -0
- data/lib/simple_bioc/relation.rb +14 -0
- data/lib/simple_bioc/sentence.rb +20 -0
- data/lib/simple_bioc/version.rb +3 -0
- data/lib/simple_bioc.rb +14 -0
- data/simple_bioc.gemspec +27 -0
- data/spec/simple_bioc_spec.rb +14 -0
- data/xml/BioC.dtd +146 -0
- data/xml/PMID-8557975-simplified-sentences-tokens.xml +492 -0
- data/xml/PMID-8557975-simplified-sentences.xml +49 -0
- data/xml/abbr.key +71 -0
- data/xml/abbr.xml +1 -0
- data/xml/ascii.key +29 -0
- data/xml/ascii.xml +3 -0
- data/xml/everything-sentence.xml +1 -0
- data/xml/everything.key +8 -0
- data/xml/everything.xml +1 -0
- data/xml/lemma.key +51 -0
- data/xml/lemma.xml +1 -0
- data/xml/pos.key +49 -0
- data/xml/pos.xml +1 -0
- data/xml/sentence.key +36 -0
- data/xml/sentence.xml +1 -0
- metadata +153 -0
data/xml/BioC.dtd
ADDED
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<!-- Combination DTD that will work with any document so far. -->
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<!--
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Some believe XML is easily read by humans and that should be
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supported by clearly formatting the elements. In the long run,
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this is destracting. While the only meaningful spaces are in text
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elements and the other spaces can be ignored, current tools add no
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additional space. Formatters and editors may be used to make the
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XML file appear more readable.
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The possible variety of annotations that one might want to produce
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or use is nearly countless. There is no guarantee that these are
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organized in the nice nested structure required for XML
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elements. Even if they were, it would be nice to more easily
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ignore unwanted annotations. So annotations are recorded in a
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stand off manner, external to the annotated text. The exceptions
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are passages and sentences because of their fundamental place in
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text.
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The text is expected to be encoded in Unicode, specifically
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utf-8. This is one of the encodings required to be implented by
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XML tools, is portable between big-endian and little-endian
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machines and is a superset of 7-bit ASCII. Code points beyond 127
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may be expressed directly in utf-8 or indirectly using numeric
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entities. Since many tools today still only directly process
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ASCII characters, conversion should be available and
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standardized. Offsets should be in 8 bit code units (bytes) for
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easier processing by naive programs.
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Nothing final. Just current thoughts.
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collection: Group of documents, usually from a larger corpus. If
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a group of documents is from several corpora, use several
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collections.
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source: Name of the source corpus from which the documents were selected
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date: Date documents extracted from original source. Can be as
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simple as yyyymmdd or an ISO timestamp.
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key: Separate file describing the types used and any other useful
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information about the data in the file. For example, if a file
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includes part-of-speech tags, this file should describe the
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part-of-speech tags used.
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infon: key-value pairs. Can record essentially arbitrary
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information. "type" will be a particular common key in the major
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sub elements below. For PubMed references, passage "type" might
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signal "title" or "abstract". For annotations, it might indicate
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"noun phrase", "gene", or "disease". In the programming language
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data structures, infons are typically represented as a map from
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strings to strings. This means keys should be unique within each
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parent element.
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document: A document in the collection. A single, complete
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stand-alone document as described by it's parent source.
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id: Typically, the id of the document in the parent
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source. Should at least be unique in the collection.
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passage: One portion of the document. For now PubMed documents
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have a title and an abstract. Structured abstracts could have
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additional passages. For a full text document, passages could be
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sections such as Introduction, Materials and Methods, or
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Conclusion. Another option would be paragraphs. Passages impose a
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linear structure on the document. Further structure in the
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document can be implied by the infon["type"] value.
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offset: Where the passage occurs in the parent document. Depending
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on the source corpus, this might be a very relevant number. They
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should be sequential and identify a passage's position in
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the document. Since pubmed is extracted from an XML file, the
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title has an offset of zero, while the abstract is assumed to
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begin after the title and one space.
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text: The original text of the passage.
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sentence: One sentence of the passage.
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offset: A document offset to where the sentence begins in the
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passage. This value is the sum of the passage offset and the local
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offset within the passage.
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text: The original text of the sentence.
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annotation: Stand-off annotation
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id: Used to refer to this annotation in relations.
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location: Location of the annotated text. Multiple locations
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indicate a multi-span annotation.
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offset: Document offset to where the annotated text begins in
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the passage or sentence. The value is the sum of the passage or
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sentence offset and the local offset within the passage or
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sentence.
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length: Length of the annotated text. While unlikely, this could
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be zero to describe an annotation that belongs between two
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characters.
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text: Unless something else is defined one would be expect the
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annotated text. The length is redundant in this case. Other uses
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for this text could be the normalized ID for a gene in a gene
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database.
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relation: Relationship between multiple annotations.
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id: Used to refer to this relation in other relationships.
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refid: Id of an annotated object or other relation.
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role: Describes how the referenced annotated object or other
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relation participates in the current relationship. Has a default
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value so can be left out if there is no meaningful value.
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-->
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<!ELEMENT collection ( source, date, key, infon*, document+ ) >
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<!ELEMENT source (#PCDATA)>
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<!ELEMENT date (#PCDATA)>
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<!ELEMENT key (#PCDATA)>
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<!ELEMENT infon (#PCDATA)>
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<!ATTLIST infon key CDATA #REQUIRED >
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<!ELEMENT document ( id, infon*, passage+, relation* ) >
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<!ELEMENT id (#PCDATA)>
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<!ELEMENT passage ( infon*, offset, ( ( text?, annotation* ) | sentence* ), relation* ) >
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<!ELEMENT offset (#PCDATA)>
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<!ELEMENT text (#PCDATA)>
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<!ELEMENT sentence ( infon*, offset, text?, annotation*, relation* ) >
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<!ELEMENT annotation ( infon*, location*, text ) >
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<!ATTLIST annotation id CDATA #IMPLIED >
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<!ELEMENT location EMPTY>
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<!ATTLIST location offset CDATA #REQUIRED >
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<!ATTLIST location length CDATA #REQUIRED >
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<!ELEMENT relation ( infon*, node* ) >
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<!ATTLIST relation id CDATA #IMPLIED >
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<!ELEMENT node EMPTY>
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<!ATTLIST node refid CDATA #REQUIRED >
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<!ATTLIST node role CDATA "" >
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@@ -0,0 +1,492 @@
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<?xml version="1.0" encoding="utf-8"?>
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<!DOCTYPE collection SYSTEM "BioC.dtd">
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<collection>
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<source>PubMed</source>
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<date>20130316</date>
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<key>PMID-8557975-simplified-sentences-tokens.key</key>
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<document>
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<id>8557975</id>
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<passage>
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<infon key="type">abstract</infon>
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<offset>0</offset>
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<sentence>
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<infon key="type">original sentence</infon>
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<offset>70</offset>
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<annotation id="t0">
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<infon key="type">token</infon>
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<location offset="70" length="6"></location>
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<text>Active</text>
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</annotation>
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<annotation id="t1">
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<infon key="type">token</infon>
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<location offset="77" length="5"></location>
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<text>Raf-1</text>
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</annotation>
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<annotation id="t2">
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<infon key="type">token</infon>
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<location offset="83" length="14"></location>
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<text>phosphorylates</text>
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</annotation>
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<annotation id="t3">
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<infon key="type">token</infon>
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<location offset="98" length="3"></location>
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<text>and</text>
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</annotation>
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<annotation id="t4">
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<infon key="type">token</infon>
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<location offset="102" length="9"></location>
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<text>activates</text>
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</annotation>
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<annotation id="t5">
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<infon key="type">token</infon>
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<location offset="112" length="3"></location>
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<text>the</text>
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</annotation>
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<annotation id="t6">
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<infon key="type">token</infon>
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<location offset="116" length="17"></location>
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<text>mitogen-activated</text>
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</annotation>
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<annotation id="t7">
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<infon key="type">token</infon>
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<location offset="134" length="7"></location>
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<text>protein</text>
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</annotation>
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<annotation id="t8">
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<infon key="type">token</infon>
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<location offset="142" length="1"></location>
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<text>(</text>
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</annotation>
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<annotation id="t9">
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<infon key="type">token</infon>
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<location offset="143" length="3"></location>
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<text>MAP</text>
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</annotation>
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<annotation id="t10">
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<infon key="type">token</infon>
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<location offset="146" length="1"></location>
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<text>)</text>
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</annotation>
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<annotation id="t11">
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<infon key="type">token</infon>
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<location offset="148" length="20"></location>
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<text>kinase/extracellular</text>
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</annotation>
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<annotation id="t12">
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<infon key="type">token</infon>
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<location offset="169" length="16"></location>
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<text>signal-regulated</text>
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</annotation>
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<annotation id="t13">
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<infon key="type">token</infon>
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<location offset="186" length="6"></location>
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<text>kinase</text>
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</annotation>
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<annotation id="t14">
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<infon key="type">token</infon>
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<location offset="193" length="6"></location>
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<text>kinase</text>
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</annotation>
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<annotation id="t15">
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<infon key="type">token</infon>
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<location offset="200" length="1"></location>
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<text>1</text>
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</annotation>
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<annotation id="t16">
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<infon key="type">token</infon>
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<location offset="202" length="1"></location>
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<text>(</text>
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</annotation>
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<annotation id="t17">
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<infon key="type">token</infon>
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<location offset="203" length="4"></location>
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<text>MEK1</text>
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</annotation>
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<annotation id="t18">
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<infon key="type">token</infon>
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<location offset="207" length="1"></location>
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<text>)</text>
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</annotation>
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<annotation id="t19">
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<infon key="type">token</infon>
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<location offset="208" length="1"></location>
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<text>,</text>
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</annotation>
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<annotation id="t20">
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<infon key="type">token</infon>
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<location offset="210" length="5"></location>
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<text>which</text>
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</annotation>
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<annotation id="t21">
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<infon key="type">token</infon>
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<location offset="216" length="2"></location>
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<text>in</text>
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</annotation>
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<annotation id="t22">
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<infon key="type">token</infon>
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<location offset="219" length="4"></location>
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<text>turn</text>
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</annotation>
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<annotation id="t23">
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<infon key="type">token</infon>
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<location offset="224" length="14"></location>
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<text>phosphorylates</text>
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</annotation>
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<annotation id="t24">
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<infon key="type">token</infon>
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<location offset="239" length="3"></location>
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<text>and</text>
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</annotation>
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<annotation id="t25">
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<infon key="type">token</infon>
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<location offset="243" length="9"></location>
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<text>activates</text>
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</annotation>
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<annotation id="t26">
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<infon key="type">token</infon>
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<location offset="253" length="3"></location>
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<text>the</text>
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</annotation>
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<annotation id="t27">
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<infon key="type">token</infon>
|
|
152
|
+
<location offset="257" length="3"></location>
|
|
153
|
+
<text>MAP</text>
|
|
154
|
+
</annotation>
|
|
155
|
+
<annotation id="t28">
|
|
156
|
+
<infon key="type">token</infon>
|
|
157
|
+
<location offset="261" length="21"></location>
|
|
158
|
+
<text>kinases/extracellular</text>
|
|
159
|
+
</annotation>
|
|
160
|
+
<annotation id="t29">
|
|
161
|
+
<infon key="type">token</infon>
|
|
162
|
+
<location offset="283" length="6"></location>
|
|
163
|
+
<text>signal</text>
|
|
164
|
+
</annotation>
|
|
165
|
+
<annotation id="t30">
|
|
166
|
+
<infon key="type">token</infon>
|
|
167
|
+
<location offset="290" length="9"></location>
|
|
168
|
+
<text>regulated</text>
|
|
169
|
+
</annotation>
|
|
170
|
+
<annotation id="t31">
|
|
171
|
+
<infon key="type">token</infon>
|
|
172
|
+
<location offset="300" length="7"></location>
|
|
173
|
+
<text>kinases</text>
|
|
174
|
+
</annotation>
|
|
175
|
+
<annotation id="t32">
|
|
176
|
+
<infon key="type">token</infon>
|
|
177
|
+
<location offset="307" length="1"></location>
|
|
178
|
+
<text>,</text>
|
|
179
|
+
</annotation>
|
|
180
|
+
<annotation id="t33">
|
|
181
|
+
<infon key="type">token</infon>
|
|
182
|
+
<location offset="309" length="4"></location>
|
|
183
|
+
<text>ERK1</text>
|
|
184
|
+
</annotation>
|
|
185
|
+
<annotation id="t34">
|
|
186
|
+
<infon key="type">token</infon>
|
|
187
|
+
<location offset="314" length="3"></location>
|
|
188
|
+
<text>and</text>
|
|
189
|
+
</annotation>
|
|
190
|
+
<annotation id="t35">
|
|
191
|
+
<infon key="type">token</infon>
|
|
192
|
+
<location offset="318" length="4"></location>
|
|
193
|
+
<text>ERK2</text>
|
|
194
|
+
</annotation>
|
|
195
|
+
<annotation id="t36">
|
|
196
|
+
<infon key="type">token</infon>
|
|
197
|
+
<location offset="322" length="1"></location>
|
|
198
|
+
<text>.</text>
|
|
199
|
+
</annotation>
|
|
200
|
+
</sentence>
|
|
201
|
+
<sentence>
|
|
202
|
+
<infon key="type">simplified sentence</infon>
|
|
203
|
+
<offset>325</offset>
|
|
204
|
+
<annotation id="t37">
|
|
205
|
+
<infon key="type">token</infon>
|
|
206
|
+
<location offset="325" length="6"></location>
|
|
207
|
+
<text>Active</text>
|
|
208
|
+
</annotation>
|
|
209
|
+
<annotation id="t38">
|
|
210
|
+
<infon key="type">token</infon>
|
|
211
|
+
<location offset="332" length="5"></location>
|
|
212
|
+
<text>Raf-1</text>
|
|
213
|
+
</annotation>
|
|
214
|
+
<annotation id="t39">
|
|
215
|
+
<infon key="type">token</infon>
|
|
216
|
+
<location offset="338" length="14"></location>
|
|
217
|
+
<text>phosphorylates</text>
|
|
218
|
+
</annotation>
|
|
219
|
+
<annotation id="t40">
|
|
220
|
+
<infon key="type">token</infon>
|
|
221
|
+
<location offset="353" length="4"></location>
|
|
222
|
+
<text>MEK1</text>
|
|
223
|
+
</annotation>
|
|
224
|
+
<annotation id="t41">
|
|
225
|
+
<infon key="type">token</infon>
|
|
226
|
+
<location offset="357" length="1"></location>
|
|
227
|
+
<text>.</text>
|
|
228
|
+
</annotation>
|
|
229
|
+
</sentence>
|
|
230
|
+
<sentence>
|
|
231
|
+
<infon key="type">simplified sentence</infon>
|
|
232
|
+
<offset>360</offset>
|
|
233
|
+
<annotation id="t42">
|
|
234
|
+
<infon key="type">token</infon>
|
|
235
|
+
<location offset="360" length="6"></location>
|
|
236
|
+
<text>Active</text>
|
|
237
|
+
</annotation>
|
|
238
|
+
<annotation id="t43">
|
|
239
|
+
<infon key="type">token</infon>
|
|
240
|
+
<location offset="367" length="5"></location>
|
|
241
|
+
<text>Raf-1</text>
|
|
242
|
+
</annotation>
|
|
243
|
+
<annotation id="t44">
|
|
244
|
+
<infon key="type">token</infon>
|
|
245
|
+
<location offset="373" length="9"></location>
|
|
246
|
+
<text>activates</text>
|
|
247
|
+
</annotation>
|
|
248
|
+
<annotation id="t45">
|
|
249
|
+
<infon key="type">token</infon>
|
|
250
|
+
<location offset="383" length="4"></location>
|
|
251
|
+
<text>MEK1</text>
|
|
252
|
+
</annotation>
|
|
253
|
+
<annotation id="t46">
|
|
254
|
+
<infon key="type">token</infon>
|
|
255
|
+
<location offset="387" length="1"></location>
|
|
256
|
+
<text>.</text>
|
|
257
|
+
</annotation>
|
|
258
|
+
</sentence>
|
|
259
|
+
<sentence>
|
|
260
|
+
<infon key="type">simplified sentence</infon>
|
|
261
|
+
<offset>390</offset>
|
|
262
|
+
<annotation id="t47">
|
|
263
|
+
<infon key="type">token</infon>
|
|
264
|
+
<location offset="390" length="4"></location>
|
|
265
|
+
<text>MEK1</text>
|
|
266
|
+
</annotation>
|
|
267
|
+
<annotation id="t48">
|
|
268
|
+
<infon key="type">token</infon>
|
|
269
|
+
<location offset="395" length="2"></location>
|
|
270
|
+
<text>in</text>
|
|
271
|
+
</annotation>
|
|
272
|
+
<annotation id="t49">
|
|
273
|
+
<infon key="type">token</infon>
|
|
274
|
+
<location offset="398" length="4"></location>
|
|
275
|
+
<text>turn</text>
|
|
276
|
+
</annotation>
|
|
277
|
+
<annotation id="t50">
|
|
278
|
+
<infon key="type">token</infon>
|
|
279
|
+
<location offset="403" length="14"></location>
|
|
280
|
+
<text>phosphorylates</text>
|
|
281
|
+
</annotation>
|
|
282
|
+
<annotation id="t51">
|
|
283
|
+
<infon key="type">token</infon>
|
|
284
|
+
<location offset="418" length="4"></location>
|
|
285
|
+
<text>ERK1</text>
|
|
286
|
+
</annotation>
|
|
287
|
+
<annotation id="t52">
|
|
288
|
+
<infon key="type">token</infon>
|
|
289
|
+
<location offset="422" length="1"></location>
|
|
290
|
+
<text>.</text>
|
|
291
|
+
</annotation>
|
|
292
|
+
</sentence>
|
|
293
|
+
<sentence>
|
|
294
|
+
<infon key="type">simplified sentence</infon>
|
|
295
|
+
<offset>425</offset>
|
|
296
|
+
<annotation id="t53">
|
|
297
|
+
<infon key="type">token</infon>
|
|
298
|
+
<location offset="425" length="4"></location>
|
|
299
|
+
<text>MEK1</text>
|
|
300
|
+
</annotation>
|
|
301
|
+
<annotation id="t54">
|
|
302
|
+
<infon key="type">token</infon>
|
|
303
|
+
<location offset="430" length="2"></location>
|
|
304
|
+
<text>in</text>
|
|
305
|
+
</annotation>
|
|
306
|
+
<annotation id="t55">
|
|
307
|
+
<infon key="type">token</infon>
|
|
308
|
+
<location offset="433" length="4"></location>
|
|
309
|
+
<text>turn</text>
|
|
310
|
+
</annotation>
|
|
311
|
+
<annotation id="t56">
|
|
312
|
+
<infon key="type">token</infon>
|
|
313
|
+
<location offset="438" length="14"></location>
|
|
314
|
+
<text>phosphorylates</text>
|
|
315
|
+
</annotation>
|
|
316
|
+
<annotation id="t57">
|
|
317
|
+
<infon key="type">token</infon>
|
|
318
|
+
<location offset="453" length="4"></location>
|
|
319
|
+
<text>ERK2</text>
|
|
320
|
+
</annotation>
|
|
321
|
+
<annotation id="t58">
|
|
322
|
+
<infon key="type">token</infon>
|
|
323
|
+
<location offset="457" length="1"></location>
|
|
324
|
+
<text>.</text>
|
|
325
|
+
</annotation>
|
|
326
|
+
</sentence>
|
|
327
|
+
<sentence>
|
|
328
|
+
<infon key="type">simplified sentence</infon>
|
|
329
|
+
<offset>460</offset>
|
|
330
|
+
<annotation id="t59">
|
|
331
|
+
<infon key="type">token</infon>
|
|
332
|
+
<location offset="460" length="4"></location>
|
|
333
|
+
<text>MEK1</text>
|
|
334
|
+
</annotation>
|
|
335
|
+
<annotation id="t60">
|
|
336
|
+
<infon key="type">token</infon>
|
|
337
|
+
<location offset="465" length="2"></location>
|
|
338
|
+
<text>in</text>
|
|
339
|
+
</annotation>
|
|
340
|
+
<annotation id="t61">
|
|
341
|
+
<infon key="type">token</infon>
|
|
342
|
+
<location offset="468" length="4"></location>
|
|
343
|
+
<text>turn</text>
|
|
344
|
+
</annotation>
|
|
345
|
+
<annotation id="t62">
|
|
346
|
+
<infon key="type">token</infon>
|
|
347
|
+
<location offset="473" length="9"></location>
|
|
348
|
+
<text>activates</text>
|
|
349
|
+
</annotation>
|
|
350
|
+
<annotation id="t63">
|
|
351
|
+
<infon key="type">token</infon>
|
|
352
|
+
<location offset="483" length="4"></location>
|
|
353
|
+
<text>ERK1</text>
|
|
354
|
+
</annotation>
|
|
355
|
+
<annotation id="t64">
|
|
356
|
+
<infon key="type">token</infon>
|
|
357
|
+
<location offset="487" length="1"></location>
|
|
358
|
+
<text>.</text>
|
|
359
|
+
</annotation>
|
|
360
|
+
</sentence>
|
|
361
|
+
<sentence>
|
|
362
|
+
<infon key="type">simplified sentence</infon>
|
|
363
|
+
<offset>489</offset>
|
|
364
|
+
<annotation id="t65">
|
|
365
|
+
<infon key="type">token</infon>
|
|
366
|
+
<location offset="489" length="4"></location>
|
|
367
|
+
<text>MEK1</text>
|
|
368
|
+
</annotation>
|
|
369
|
+
<annotation id="t66">
|
|
370
|
+
<infon key="type">token</infon>
|
|
371
|
+
<location offset="494" length="2"></location>
|
|
372
|
+
<text>in</text>
|
|
373
|
+
</annotation>
|
|
374
|
+
<annotation id="t67">
|
|
375
|
+
<infon key="type">token</infon>
|
|
376
|
+
<location offset="497" length="4"></location>
|
|
377
|
+
<text>turn</text>
|
|
378
|
+
</annotation>
|
|
379
|
+
<annotation id="t68">
|
|
380
|
+
<infon key="type">token</infon>
|
|
381
|
+
<location offset="502" length="9"></location>
|
|
382
|
+
<text>activates</text>
|
|
383
|
+
</annotation>
|
|
384
|
+
<annotation id="t69">
|
|
385
|
+
<infon key="type">token</infon>
|
|
386
|
+
<location offset="512" length="4"></location>
|
|
387
|
+
<text>ERK2</text>
|
|
388
|
+
</annotation>
|
|
389
|
+
<annotation id="t70">
|
|
390
|
+
<infon key="type">token</infon>
|
|
391
|
+
<location offset="516" length="1"></location>
|
|
392
|
+
<text>.</text>
|
|
393
|
+
</annotation>
|
|
394
|
+
</sentence>
|
|
395
|
+
<!-- equ -->
|
|
396
|
+
<!-- Active -->
|
|
397
|
+
<relation id="r0">
|
|
398
|
+
<infon key="type">equ</infon>
|
|
399
|
+
<node refid="t0" role="original"></node>
|
|
400
|
+
<node refid="t37" role="simplified"></node>
|
|
401
|
+
<node refid="t42" role="simplified"></node>
|
|
402
|
+
</relation>
|
|
403
|
+
<!-- RAF-1 -->
|
|
404
|
+
<relation id="r1">
|
|
405
|
+
<infon key="type">equ</infon>
|
|
406
|
+
<node refid="t1" role="original"></node>
|
|
407
|
+
<node refid="t38" role="simplified"></node>
|
|
408
|
+
<node refid="t43" role="simplified"></node>
|
|
409
|
+
</relation>
|
|
410
|
+
<!-- phosphorylates -->
|
|
411
|
+
<relation id="r2">
|
|
412
|
+
<infon key="type">equ</infon>
|
|
413
|
+
<node refid="t2" role="original"></node>
|
|
414
|
+
<node refid="t39" role="simplified"></node>
|
|
415
|
+
</relation>
|
|
416
|
+
<!-- MEK1 -->
|
|
417
|
+
<relation id="r3">
|
|
418
|
+
<infon key="type">equ</infon>
|
|
419
|
+
<node refid="t17" role="original"></node>
|
|
420
|
+
<node refid="t40" role="simplified"></node>
|
|
421
|
+
<node refid="t45" role="simplified"></node>
|
|
422
|
+
<node refid="t47" role="simplified"></node>
|
|
423
|
+
<node refid="t53" role="simplified"></node>
|
|
424
|
+
<node refid="t59" role="simplified"></node>
|
|
425
|
+
<node refid="t65" role="simplified"></node>
|
|
426
|
+
</relation>
|
|
427
|
+
<!-- . -->
|
|
428
|
+
<relation id="r4">
|
|
429
|
+
<infon key="type">equ</infon>
|
|
430
|
+
<node refid="t36" role="original"></node>
|
|
431
|
+
<node refid="t41" role="simplified"></node>
|
|
432
|
+
<node refid="t46" role="simplified"></node>
|
|
433
|
+
<node refid="t52" role="simplified"></node>
|
|
434
|
+
<node refid="t58" role="simplified"></node>
|
|
435
|
+
<node refid="t64" role="simplified"></node>
|
|
436
|
+
<node refid="t70" role="simplified"></node>
|
|
437
|
+
</relation>
|
|
438
|
+
<!-- activates -->
|
|
439
|
+
<relation id="r5">
|
|
440
|
+
<infon key="type">equ</infon>
|
|
441
|
+
<node refid="t4" role="original"></node>
|
|
442
|
+
<node refid="t44" role="simplified"></node>
|
|
443
|
+
</relation>
|
|
444
|
+
<!-- in -->
|
|
445
|
+
<relation id="r6">
|
|
446
|
+
<infon key="type">equ</infon>
|
|
447
|
+
<node refid="t21" role="original"></node>
|
|
448
|
+
<node refid="t48" role="simplified"></node>
|
|
449
|
+
<node refid="t54" role="simplified"></node>
|
|
450
|
+
<node refid="t60" role="simplified"></node>
|
|
451
|
+
<node refid="t66" role="simplified"></node>
|
|
452
|
+
</relation>
|
|
453
|
+
<!-- turn -->
|
|
454
|
+
<relation id="r7">
|
|
455
|
+
<infon key="type">equ</infon>
|
|
456
|
+
<node refid="t22" role="original"></node>
|
|
457
|
+
<node refid="t49" role="simplified"></node>
|
|
458
|
+
<node refid="t55" role="simplified"></node>
|
|
459
|
+
<node refid="t61" role="simplified"></node>
|
|
460
|
+
<node refid="t67" role="simplified"></node>
|
|
461
|
+
</relation>
|
|
462
|
+
<!-- phosphorylates -->
|
|
463
|
+
<relation id="r8">
|
|
464
|
+
<infon key="type">equ</infon>
|
|
465
|
+
<node refid="t23" role="original"></node>
|
|
466
|
+
<node refid="t50" role="simplified"></node>
|
|
467
|
+
<node refid="t56" role="simplified"></node>
|
|
468
|
+
</relation>
|
|
469
|
+
<!-- ERK1 -->
|
|
470
|
+
<relation id="r9">
|
|
471
|
+
<infon key="type">equ</infon>
|
|
472
|
+
<node refid="t33" role="original"></node>
|
|
473
|
+
<node refid="t51" role="simplified"></node>
|
|
474
|
+
<node refid="t63" role="simplified"></node>
|
|
475
|
+
</relation>
|
|
476
|
+
<!-- ERK2 -->
|
|
477
|
+
<relation id="r10">
|
|
478
|
+
<infon key="type">equ</infon>
|
|
479
|
+
<node refid="t35" role="original"></node>
|
|
480
|
+
<node refid="t57" role="simplified"></node>
|
|
481
|
+
<node refid="t69" role="simplified"></node>
|
|
482
|
+
</relation>
|
|
483
|
+
<!-- activates -->
|
|
484
|
+
<relation id="r11">
|
|
485
|
+
<infon key="type">equ</infon>
|
|
486
|
+
<node refid="t25" role="original"></node>
|
|
487
|
+
<node refid="t62" role="simplified"></node>
|
|
488
|
+
<node refid="t68" role="simplified"></node>
|
|
489
|
+
</relation>
|
|
490
|
+
</passage>
|
|
491
|
+
</document>
|
|
492
|
+
</collection>
|