added notes from genome api discussion

genome_api_notes.md

@@ -0,0 +1,40 @@
+# Genome API
+
+Data model
+
+    +-------+   +--------+   +-------------+                  
+    | Genome+-> |Features+-->+Feature      +-+----->Amino+acid
+    +----+--+   +--------+   |sequences    | |                
+         |                   +------+------+ |                
+         |                          |        +----->DNA       
+         |                          |                         
+     +---+-------+                  |                         
+     | ContigSet +<-----------------+                         
+     +-----------+    position info                           
+
+## Taxonomy
+
+* lineage - list of descriptors
+* taxonomy - string
+* taxonomic id - string
+
+## Sequence
+
+* get_contig(id, start?, stop?, strand?)
+* list of contigs
+* list of DNA or AA features, e.g. get_feature_dna(feature_id)
+
+## Annotation
+
+???
+
+## Metadata
+
+* quality score. multidimensional
+* circular (true, false, unknown)
+* type: 'draft' or 'finished'
+* reference
+* date of origination
+* external resource (see identifiers)
+* percent assembled
+* number of contigs

src/data_api/search.py

@@ -28,3 +28,32 @@ class DataModel(SearchableData):
     """
     pass
 
+"""
+WIP
+"""
+from .semantics import Type
+
+class Node(object):
+    def __init__(self, type_=None):
+        """
+        :type type_: Type
+        """
+        self._type = type_
+
+    def get(self, subset=()):
+        """Projection operator."""
+        return [getattr(self, name) for name in subset]
+
+    def find_related(self, node_type=None, edge_type=None,
+                     node_filter=None, edge_filter=None, max_depth=0):
+        """Find all related nodes of type `node_type` that are related
+        by edges of type `edge_type`. Filter nodes and edges according to
+        values in `node_filter` and `edge_filter`.
+        Look `max_depth` nodes away from the origin, with values <= 0
+        meaning no limit.
+
+        :return: List of Node
+        """
+        pass
+
+