Module ImportFrom alias ImportFrom alias ClassDef bases NameLoad body Pass decorator_list FunctionDef arguments args NameParam defaults body ImportFrom alias Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Str Index Num Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body ImportFrom alias ImportFrom alias Assign NameStore Call NameLoad NameLoad Assign NameStore SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Str Index Num Assign NameStore Call NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults Dict body Import alias identifier TryExcept body Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword Num Return NameLoad handlers ExceptHandler type AttributeLoad NameLoad attr body Return Str ExceptHandler type AttributeLoad NameLoad attr body Return Str decorator_list FunctionDef arguments args NameParam defaults body Import alias Assign NameStore Dict Str Str TryExcept body Return Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad handlers ExceptHandler type NameLoad body Return Dict decorator_list ClassDef bases NameLoad body Assign NameStore NameLoad Assign NameStore Str FunctionDef arguments args NameParam defaults kwarg body Expr Call AttributeLoad NameLoad attr NameLoad Str NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return ListLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults kwarg body Expr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad For NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam defaults kwarg body Assign NameStore Dict Str Str Str Str AttributeLoad NameLoad attr AttributeLoad NameLoad attr BinOpAdd SubscriptLoad AttributeLoad NameLoad attr Index Str Str BinOpAdd SubscriptLoad AttributeLoad NameLoad attr Index Str Str Assign NameStore Str decorator_list FunctionDef arguments args NameParam defaults kwarg body Return ListLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad kwarg body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr keyword NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword NameLoad Expr Call NameLoad keyword NameLoad Assign NameStore TupleLoad Str Str Assign NameStore TupleLoad Str Str Str Str Str Assign AttributeStore NameLoad attr TupleLoad Str Str Str Str For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword NameLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad If CompareIsNot NameLoad NameLoad body Assign SubscriptStore AttributeLoad NameLoad attr Index Str NameLoad orelse If CompareIsNot NameLoad NameLoad body Assign SubscriptStore AttributeLoad NameLoad attr Index Str NameLoad If CompareIn Str AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str If CompareIsNot NameLoad NameLoad body Assign SubscriptStore AttributeLoad NameLoad attr Index Str NameLoad orelse If CompareIsNot NameLoad NameLoad body Assign SubscriptStore AttributeLoad NameLoad attr Index Str NameLoad orelse If CompareIsNot NameLoad NameLoad body Assign SubscriptStore AttributeLoad NameLoad attr Index Str NameLoad If CompareIn Str AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str If CompareIsNot NameLoad NameLoad body Assign SubscriptStore AttributeLoad NameLoad attr Index Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad If CompareIsNot NameLoad NameLoad body Assign SubscriptStore AttributeLoad NameLoad attr Index Str NameLoad If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad orelse If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad Expr Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body If AttributeLoad Call NameLoad NameLoad NameLoad attr body Return NameLoad orelse For NameStore AttributeLoad NameLoad attr body If Call AttributeLoad Call NameLoad NameLoad NameLoad attr body Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body If AttributeLoad Call NameLoad NameLoad NameLoad attr body Return Call AttributeLoad Call NameLoad NameLoad NameLoad attr For NameStore AttributeLoad NameLoad attr body Assign NameStore Call NameLoad NameLoad NameLoad If Call AttributeLoad NameLoad attr body Assign NameStore BinOpAdd BinOpAdd Call NameLoad NameLoad Str Call AttributeLoad Call AttributeLoad SubscriptLoad AttributeLoad NameLoad attr Index Num attr attr Return Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Str FunctionDef arguments args NameParam NameParam defaults body Return Call NameLoad BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str NameLoad decorator_list Assign NameStore Call NameLoad NameLoad Str If CompareIn Str NameLoad body Assign NameStore SubscriptLoad NameLoad Index Str If CompareIn Str NameLoad body Expr Call AttributeLoad NameLoad attr ListComp SubscriptLoad NameLoad Index Str comprehension NameStore SubscriptLoad NameLoad Index Str orelse If CompareIn Str NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Index Str Assign NameStore Call NameLoad NameLoad Str If CompareIn Str NameLoad body Assign NameStore SubscriptLoad NameLoad Index Str If CompareIn Str NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index Str Index Str orelse If CompareIn Str NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Index Str decorator_list FunctionDef arguments args NameParam defaults body FunctionDef arguments args NameParam defaults body Import alias identifier Assign NameStore Dict Str NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Return Call NameLoad BinOpMod Str NameLoad decorator_list Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Str If CompareEq SubscriptLoad NameLoad Slice Num Str body Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad If CompareGt Call NameLoad NameLoad Num body Assign NameStore Call AttributeLoad SubscriptLoad SubscriptLoad NameLoad Index Num Index Str attr Str Assign NameStore GeneratorExp Call AttributeLoad NameLoad attr Str comprehension NameStore NameLoad Assign NameStore ListComp ListComp Call AttributeLoad Call AttributeLoad NameLoad attr Str Str attr comprehension NameStore NameLoad comprehension NameStore NameLoad Assign NameStore ListComp SubscriptLoad NameLoad Index Num comprehension NameStore NameLoad CompareEq SubscriptLoad NameLoad Index Num Str For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad If CompareGt Call NameLoad NameLoad Num body Assign NameStore SubscriptLoad NameLoad Index Num If CompareIn Str NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str If CompareIn Str NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str decorator_list FunctionDef arguments args NameParam defaults body FunctionDef arguments args NameParam defaults body Import alias identifier Assign NameStore Str Assign NameStore BinOpAdd NameLoad BinOpMod Str NameLoad Return Call AttributeLoad NameLoad attr Call NameLoad NameLoad decorator_list Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Str If CompareEq SubscriptLoad NameLoad Slice Num Str body Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad For NameStore Call AttributeLoad NameLoad attr Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list decorator_list
N/A PyOpenWorm.pProperty Property PyOpenWorm.dataObject DataObject EvidenceError N/A Exception N/A N/A N/A _pubmed_uri_to_pmid N/A N/A uri N/A N/A urlparse urlparse N/A parsed N/A urlparse uri N/A pmid N/A int N/A N/A N/A N/A parsed path split / N/A 2 N/A pmid N/A _doi_uri_to_doi N/A N/A uri N/A N/A urlparse urlparse urllib2 unquote N/A parsed N/A urlparse uri N/A doi N/A N/A N/A N/A parsed path split / N/A 1 N/A doi N/A unquote doi N/A doi N/A _url_request N/A N/A url headers N/A N/A N/A N/A urllib2 U N/A N/A N/A r N/A N/A U Request url headers headers N/A s N/A N/A U urlopen r timeout 1 N/A s N/A N/A N/A N/A U HTTPError N/A N/A N/A N/A N/A U URLError N/A N/A N/A _json_request N/A N/A url N/A N/A N/A json N/A headers N/A Content-Type application/json N/A N/A N/A N/A N/A json load N/A _url_request url headers N/A N/A N/A BaseException N/A N/A N/A N/A AssertsAllAbout N/A Property N/A N/A multiple True N/A linkName asserts_all_about __init__ N/A N/A self N/A kwargs N/A N/A N/A N/A Property __init__ self asserts_all_about kwargs N/A values N/A N/A self N/A N/A N/A N/A N/A property set N/A N/A self o N/A kwargs N/A N/A Establish the "asserts" relationship for all of the properties of the given object N/A N/A N/A N/A self owner asserts o N/A p N/A o properties N/A N/A N/A N/A N/A self owner asserts p N/A get N/A N/A self N/A kwargs N/A N/A ns N/A ow ns1 ev ns2 N/A self base_namespace N/A self rdf_namespace N/A N/A N/A self base_namespace N/A Evidence / N/A N/A N/A self base_namespace N/A SimpleProperty / N/A q 
        SELECT ?DataObject ?x ?prop WHERE
        {
            ?DataObject rdf:type ow:DataObject .
            ?DataObject ?x ?DataObject_prop .
            ?DataObject_prop sp:value ?prop .
            ?Evidence ev:asserts ?Evidence_asserts .
            filter (EXISTS { ?DataObject_prop rdf:type ow:Property . })
        # object
        # asserts property pattern
        # general property pattern
        }
         N/A triples N/A N/A self N/A kwargs N/A N/A N/A N/A N/A Evidence N/A DataObject N/A N/A 
    A representation of some document which provides evidence like scholarly
    references, for other objects.

    Possible keys include::

        pmid,pubmed: a pubmed id or url (e.g., 24098140)
        wbid,wormbase: a wormbase id or url (e.g., WBPaper00044287)
        doi: a Digitial Object id or url (e.g., s00454-010-9273-0)

    Attaching evidence
    -------------------
    Attaching evidence to an object is as easy as::

          e = Evidence(author='White et al.', date='1986')
          e.asserts(Connection(pre_cell="VA11", post_cell="VD12"))
          e.save()

    But what does this series of statements mean? For us it means that White et al.
    assert that "the cells VA11 and VD12 have a connection".
    In particular, it says nothing about the neurons themselves.

    Another example::

          e = Evidence(author='Sulston et al.', date='1983')
          e.asserts(Neuron(name="AVDL").lineageName("AB alaaapalr"))
          e.save()

    This would say that Sulston et al. claimed that neuron AVDL has lineage AB alaaapalr.

    Now a more ambiguous example::

          e = Evidence(author='Sulston et al.', date='1983')
          e.asserts(Neuron(name="AVDL"))
          e.save()

    What might this mean? There's no clear relationship being discussed as in the
    previous examples. There are two reasonable semantics for
    these statements. They could indicate that Sulston et al. assert everything
    about the AVDL (in this case, only its name). Or they could
    indicate that Sulston et al. state the existence of AVDL. We will assume the
    semantics of the latter for *most* objects. The second
    intention can be expressed as::

          e = Evidence(author='Sulston et al.', date='1983')
          e.asserts_all_about(Neuron(name="AVDL"))
          e.save()

    `asserts_all_about` individually asserts each of the properties of the Neuron
    including its existence. It does not recursively assert
    properties of values set on the AVDL Neuron. If, for instance, the Neuron had a
    *complex object* as the value for its receptor types with
    information about the receptor's name primary agonist, etc., `asserts_all_about`
      would say nothing about these. However, `asserts_all` (TODO)::

          e.asserts_all(Neuron(name="AVDL",receptor=complex_receptor_object))

    would make the aforementioned recursive statement.

    Retrieving evidence
    -------------------

    .. Not tested with the latest

    Retrieving evidence for an object is trivial as well ::

          e = Evidence()
          e.asserts(Connection(pre_cell="VA11", post_cell="VD12"))
          for x in e.load():
             print x

    This would print all of the evidence for the connection between VA11 and VD12

    It's important to note that the considerations of recursive evidence assertions
    above do not operate for retrieval. Only evidence for the
    particular object queried (the Connection in the example above), would be
    returned and not any evidence for anything otherwise about VA11
    or VD12.

    Attributes
    ----------
    asserts : ObjectProperty (value_type=DataObject)
       When used with an argument, state that this Evidence asserts that the
       relationship is true.

       Example::

           import bibtex
           bt = bibtex.parse("my.bib")
           n1 = Neuron("AVAL")
           n2 = Neuron("DA3")
           c = Connection(pre=n1,post=n2,class="synapse")
           e = Evidence(bibtex=bt['white86'])
           e.asserts(c)

       Other methods return objects which asserts accepts.

       Example::

           n1 = Neuron("AVAL")
           r = n1.neighbor("DA3")
           e = Evidence(bibtex=bt['white86'])
           e.asserts(r)

       When used without arguments, returns a sequence of statements asserted by
       this evidence

       Example::

           import bibtex
           bt = bibtex.parse("my.bib")
           n1 = Neuron("AVAL")
           n2 = Neuron("DA3")
           c = Connection(pre=n1,post=n2,class="synapse")
           e = Evidence(bibtex=bt['white86'])
           e.asserts(c)
           list(e.asserts()) # Returns a list [..., d, ...] such that d==c
    doi : DatatypeProperty
        A Digital Object Identifier (DOI) that provides evidence, optional
    pmid : DatatypeProperty
        A PubMed ID (PMID) that point to a paper that provides evidence, optional
    wormbaseid : DatatypeProperty
        An ID from WormBase that points to a record that provides evidence, optional
    author : DatatypeProperty
        The author of the evidence
    title : DatatypeProperty
        The title of the evidence
    year : DatatypeProperty
        The date (e.g., publication date) of the evidence
    uri : DatatypeProperty
        A URL that points to evidence

    Parameters
    ----------
    doi : string
        A Digital Object Identifier (DOI) that provides evidence, optional
    pmid : string
        A PubMed ID (PMID) that point to a paper that provides evidence, optional
    wormbaseid : string
        An ID from WormBase that points to a record that provides evidence, optional
    author : string
        The author of the evidence
    title : string
        The title of the evidence
    year : string or int
        The date (e.g., publication date) of the evidence
    uri : string
        A URL that points to evidence
     __init__ N/A N/A self conf author uri year date title doi wbid wormbaseid wormbase bibtex pmid pubmed N/A False None None None None None None None None None None None None kwargs N/A N/A N/A N/A N/A super Evidence self __init__ conf conf kwargs N/A N/A self _fields N/A dict N/A N/A N/A Evidence ObjectProperty asserts multiple True owner self N/A N/A AssertsAllAbout owner self N/A multivalued_fields N/A author uri N/A other_fields N/A year title doi wbid pmid N/A N/A self id_precedence N/A doi pmid wbid uri N/A x multivalued_fields N/A N/A N/A N/A Evidence DatatypeProperty x multiple True owner self N/A x other_fields N/A N/A N/A N/A Evidence DatatypeProperty x owner self N/A N/A pmid None N/A N/A N/A N/A self _fields N/A pmid pmid N/A N/A N/A pubmed None N/A N/A N/A N/A self _fields N/A pmid pubmed N/A N/A pmid N/A self _fields N/A N/A N/A N/A self _pubmed_extract N/A N/A N/A self pmid N/A N/A self _fields N/A pmid N/A N/A wbid None N/A N/A N/A N/A self _fields N/A wormbase wbid N/A N/A N/A wormbase None N/A N/A N/A N/A self _fields N/A wormbase wormbase N/A N/A N/A wormbaseid None N/A N/A N/A N/A self _fields N/A wormbase wormbaseid N/A N/A wormbase N/A self _fields N/A N/A N/A N/A self _wormbase_extract N/A N/A N/A self wbid N/A N/A self _fields N/A wormbase N/A N/A doi None N/A N/A N/A N/A self _fields N/A doi doi N/A N/A N/A self _crossref_doi_extract N/A N/A N/A self doi doi N/A N/A bibtex None N/A N/A N/A N/A self _fields N/A bibtex bibtex N/A N/A year None N/A N/A N/A N/A self year year N/A N/A N/A date None N/A N/A N/A N/A self year date N/A N/A title None N/A N/A N/A N/A self title title N/A N/A author None N/A N/A N/A N/A self author author N/A add_data N/A N/A self k v N/A N/A N/A  Add a field

        Parameters
        ----------
        k : string
            Field name
        v : string
            Field value
         N/A N/A N/A self _fields N/A k v N/A dp N/A N/A Evidence DatatypeProperty k owner self N/A N/A dp v N/A defined N/A N/A self N/A N/A N/A N/A N/A super Evidence self defined N/A N/A True N/A N/A x N/A self id_precedence N/A N/A N/A N/A N/A getattr self x has_defined_value N/A N/A True N/A property identifier N/A N/A self N/A N/A N/A N/A N/A super Evidence self defined N/A N/A N/A N/A N/A super Evidence self identifier N/A idKind N/A self id_precedence N/A N/A idprop N/A getattr self idKind N/A N/A N/A idprop has_defined_value N/A N/A s N/A N/A N/A str idKind : N/A N/A N/A N/A N/A N/A idprop defined_values N/A 0 identifier n3 N/A N/A N/A self make_identifier s N/A _wormbase_extract N/A N/A self N/A N/A N/A wbid N/A N/A self _fields N/A wormbase wbRequest N/A N/A ident field N/A N/A N/A N/A _json_request N/A N/A N/A http://api.wormbase.org/rest/widget/paper/ wbid / field N/A N/A j N/A wbRequest wbid authors N/A N/A fields j N/A N/A f N/A j N/A fields N/A N/A data f N/A N/A N/A N/A self author N/A N/A x N/A label N/A x N/A f N/A data N/A N/A N/A name f N/A N/A N/A N/A self author N/A N/A N/A f N/A name N/A data N/A label N/A j N/A wbRequest wbid publication_date N/A N/A fields j N/A N/A f N/A j N/A fields N/A N/A data f N/A N/A N/A N/A self year N/A N/A f N/A data N/A label N/A N/A N/A name f N/A N/A N/A N/A self year N/A N/A N/A f N/A name N/A data N/A label N/A _crossref_doi_extract N/A N/A self N/A N/A crRequest N/A N/A doi N/A N/A N/A urllib U N/A data N/A q doi N/A data_encoded N/A N/A U urlencode data N/A N/A _json_request N/A http://search.labs.crossref.org/dois?%s data_encoded N/A N/A doi N/A N/A self _fields N/A doi N/A N/A N/A doi N/A 4 http N/A N/A doi N/A _doi_uri_to_doi doi N/A r N/A crRequest doi N/A N/A N/A len r 0 N/A N/A extra_data N/A N/A N/A N/A r N/A 0 N/A coins split &amp; N/A fields N/A N/A N/A x split = N/A x extra_data N/A fields N/A N/A N/A N/A N/A N/A y replace + strip N/A y x N/A x fields N/A authors N/A N/A x N/A 1 N/A x fields N/A N/A x N/A 0 rft.au N/A a authors N/A N/A N/A N/A self author a N/A N/A N/A len r 0 N/A N/A r N/A r N/A 0 N/A N/A title r N/A N/A N/A N/A self title N/A r N/A title N/A N/A year r N/A N/A N/A N/A self year N/A r N/A year N/A _pubmed_extract N/A N/A self N/A N/A pmRequest N/A N/A pmid N/A N/A N/A xml.etree.ElementTree ET N/A base http://eutils.ncbi.nlm.nih.gov/entrez/eutils/ N/A url N/A base N/A esummary.fcgi?db=pubmed&id=%d pmid N/A N/A N/A ET parse N/A _url_request url N/A N/A pmid N/A N/A self _fields N/A pmid N/A N/A N/A pmid N/A 4 http N/A N/A pmid N/A _pubmed_uri_to_pmid pmid N/A pmid N/A int pmid N/A tree N/A pmRequest pmid N/A x N/A N/A tree findall ./DocSum/Item[@Name="AuthorList"]/Item N/A N/A N/A N/A self author N/A x text N/A N/A