EDAM manager skeleton

edam_manager.py

@@ -0,0 +1,57 @@
+
+
+class edam_manager(object):
+
+    def __init__(self):
+        # ontology parsing happens here
+        pass
+
+    def get_terms_by_name(self, name):
+        """
+        query for ontological terms by name
+        :param name: str
+        :return: collection of term
+        """
+        pass
+
+    def common_ancestors(self, term1, term2):
+        """
+        returns the terms that are the least common ancestors of the given two terms
+        :param term1:
+        :param term2:
+        :return: collection of term
+        """
+        pass
+
+    def is_placeholder(self, term):
+        """
+        checks if a term is a real term or a placeholder created for structuring purposes.
+        :param term:
+        :return: True if the term is an organisational entity (e.g., alignment, 'phylogenetic data')
+        or False if it is a real term (e.g., 'sequence alignment', 'phylogenetic tree').
+        """
+        pass
+
+    def format2data(self, term):
+        """
+        given a format term returns the corresponding data terms, e.g. given 'newick' returns 'phylogenetic tree'.
+        :param term: format term
+        :return: collection of data term
+        """
+        pass
+
+    def get_description(self, term):
+        """
+        returns the term description
+        :param term:
+        :return: str
+        """
+        pass
+
+    def get_term_by_id(self, id):
+        """
+        query for an ontological term by id
+        :param id: str
+        :return: term
+        """
+        pass