Vagus scaffold initial publication

src/scaffoldmaker/annotation/vagus_terms.py

@@ -0,0 +1,247 @@
+"""
+Common resource for vagus annotation terms.
+"""
+
+# convention: preferred name, preferred id, followed by any other ids and alternative names
+vagus_marker_terms = [
+    # anatomical landmarks
+    ("level of superior border of jugular foramen on the vagus nerve", "ILX:0794617"),
+    ("right level of superior border of jugular foramen on the vagus nerve", "ILX:0794618"),
+    ("left level of superior border of jugular foramen on the vagus nerve", "ILX:0794619"),
+    ("level of inferior border of jugular foramen on the vagus nerve", "ILX:0794620"),
+    ("right level of inferior border of jugular foramen on the vagus nerve", "ILX:0794621"),
+    ("left level of inferior border of jugular foramen on the vagus nerve", "ILX:0794622"),
+    ("level of inferior border of cranium on the vagus nerve", "ILX:0794623"),
+    ("right level of inferior border of cranium on the vagus nerve", "ILX:0794624"),
+    ("left level of inferior border of cranium on the vagus nerve", "ILX:0794625"),
+    ("level of C1 transverse process on the vagus nerve", "ILX:0794626"),
+    ("right level of C1 transverse process on the vagus nerve", "ILX:0794627"),
+    ("left level of C1 transverse process on the vagus nerve", "ILX:0794628"),
+    ("level of greater horn of hyoid on the vagus nerve", "ILX:0794629"),
+    ("right level of greater horn of hyoid on the vagus nerve", "ILX:0794630"),
+    ("left level of greater horn of hyoid on the vagus nerve", "ILX:0794631"),
+    ("level of laryngeal prominence on the vagus nerve", "ILX:0794632"),
+    ("right level of laryngeal prominence on the vagus nerve", "ILX:0794633"),
+    ("left level of laryngeal prominence on the vagus nerve", "ILX:0794634"),
+    ("level of angle of the mandible on the vagus nerve", "ILX:0794635"),
+    ("right level of angle of the mandible on the vagus nerve", "ILX:0794636"),
+    ("left level of angle of the mandible on the vagus nerve", "ILX:0794637"),
+    ("level of carotid bifurcation on the vagus nerve", "ILX:0794638"),
+    ("right level of carotid bifurcation on the vagus nerve", "ILX:0794639"),
+    ("left level of carotid bifurcation on the vagus nerve", "ILX:0794640"),
+    ("level of superior border of the clavicle on the vagus nerve", "ILX:0794641"),
+    ("right level of superior border of the clavicle on the vagus nerve", "ILX:0794642"),
+    ("left level of superior border of the clavicle on the vagus nerve", "ILX:0794643"),
+    ("level of jugular notch on the vagus nerve", "ILX:0794644"),
+    ("right level of jugular notch on the vagus nerve", "ILX:0794645"),
+    ("left level of jugular notch on the vagus nerve", "ILX:0794646"),
+    #("level of carina", "None"),
+    #("right level of carina", "None"),
+    #("left level of carina", "None"),
+    ("level of sternal angle on the vagus nerve", "ILX:0794647"),
+    ("right level of sternal angle on the vagus nerve", "ILX:0794648"),
+    ("left level of sternal angle on the vagus nerve", "ILX:0794649"),
+    ("level of 1 cm superior to start of esophageal plexus on the vagus nerve", "ILX:0794650"),  # !!!
+    ("right level of 1 cm superior to start of esophageal plexus on the vagus nerve", "ILX:0794651"),  # !!!
+    ("left level of 1 cm superior to start of esophageal plexus on the vagus nerve", "ILX:0794652"),  # !!!
+    ("level of esophageal hiatus on the vagus nerve", "ILX:0794653"),
+    ("right level of esophageal hiatus on the vagus nerve", "ILX:0794654"),
+    ("left level of esophageal hiatus on the vagus nerve", "ILX:0794655"),
+    ("level of aortic hiatus on the vagus nerve", "ILX:0794656"),
+    ("right level of aortic hiatus on the vagus nerve", "ILX:0794657"),
+    ("left level of aortic hiatus on the vagus nerve", "ILX:0794658"),
+]
+
+vagus_branch_terms = [
+    # branch names, based on lit.review
+    # branch names with no indication of the side
+    ("meningeal branch of vagus nerve", "FMA:6231"),
+    ("communicating branch of vagus nerve with glossopharyngeal nerve", "FMA:6233"),
+    ("auricular branch of vagus nerve", "FMA:6232"),
+    ("pharyngeal branch of vagus nerve", "UBERON:0000929"),
+    ("lingual branch of vagus nerve", "FMA:6235"),
+    ("branch of vagus nerve to carotid body", "FMA:6237"),
+    ("communicating branch of superior cervical ganglion with vagus nerve", "FMA:6901"),
+    ("superior laryngeal nerve", "UBERON:0011326"),
+    ("internal laryngeal nerve", "FMA:6240"),
+    ("external branch of superior laryngeal nerve", "FMA:6243"),
+    ("communicating branch of internal laryngeal nerve with recurrent laryngeal nerve", "FMA:53544"),
+    ("communicating branch of external laryngeal nerve with superior cardiac nerve", "FMA:6708"),
+    ("pulmonary branch of vagus nerve", "FMA:65515"),
+    ("bronchial branch of vagus nerve", "FMA:6247"),
+    ("superior cervical cardiac branch of vagus nerve", "FMA:6244"),
+    ("recurrent laryngeal nerve", "UBERON:0003716"),
+    ("extra-laryngeal branch of recurrent laryngeal nerve to larynx", "FMA:6710"),
+    ("oesophageal branch of recurrent laryngeal nerve", "FMA:6248"),
+    ("tracheal branch of recurrent laryngeal nerve", "FMA:6249"),
+    ("inferior laryngeal nerve", "UBERON:0003716"), # same code as for recurrent laryngeal nerve
+    ("communicating branch of recurrent laryngeal nerve with internal laryngeal nerve", "FMA:53526"),
+    ("inferior cervical cardiac branch of vagus nerve", "FMA:75530"),
+    ("thoracic cardiac branch of vagus nerve", "FMA:53601"),
+
+    # right vagus branches
+    ("right vagus nerve", "FMA:6219"),
+    ("right vagus X nerve trunk", "UBERON:0035021"),
+    ("meningeal branch of right vagus nerve", "FMA:53541"),
+    ("recurrent meningeal branch of right vagus nerve", "None"),
+    ("communicating branch of right vagus nerve with right glossopharyngeal nerve", "FMA:52559"),
+    ("auricular branch of right vagus nerve", "FMA:53534"),
+    ("communicating branch of auricular branch of right vagus nerve with right facial nerve", "FMA:53587"),
+    ("communicating branch of auricular branch of right vagus nerve with right posterior auricular nerve", "FMA:53589"),
+    ("pharyngeal branch of right vagus nerve to pharyngeal nerve plexus", "FMA:53635"),
+    ("lingual branch of right vagus nerve", "FMA:53633"),
+    ("communicating branch of pharyngeal branch of right vagus nerve with superior cervical ganglion", "None"),
+    ("branch of right vagus nerve to carotid body", "FMA:53606"),
+    ("communicating branch of superior cervical ganglion with right vagus nerve", "ILX:0794055"),
+    ("right superior laryngeal nerve", "FMA:53530"),
+    ("right internal laryngeal nerve", "FMA:53539"),
+    ("right external laryngeal nerve", "FMA:53537"),
+    ("superior branch of right internal laryngeal nerve", "FMA:53575"), # generic term???
+    ("middle branch of right internal laryngeal nerve", "None"),
+    ("inferior branch of right internal laryngeal nerve", "FMA:53581"), # generic term???
+    ("communicating branch of right internal laryngeal nerve with right recurrent laryngeal nerve", "FMA:53571"),
+    ("communicating branch of right external laryngeal nerve with right superior cardiac nerve", "FMA:53561"),
+    ("cardiopulmonary branch A of right vagus nerve", "ILX:0794154"),
+    ("cardiopulmonary branch B of right vagus nerve", "ILX:0794155"),
+    ("pulmonary branch of right vagus nerve", "FMA:6671"),
+    ("pulmonary branch A of right vagus nerve", "None"),
+    ("pulmonary branch B of right vagus nerve", "None"),
+    ("pulmonary branch C of right vagus nerve", "None"),
+    ("pulmonary branch D of right vagus nerve", "None"),
+    ("pulmonary branch E of right vagus nerve", "None"),
+    # === temporary branches used in the japanese dataset
+    ("right A lateral pulmonary branch of vagus nerve", "ILX:0794278"),
+    ("right B lateral pulmonary branch of vagus nerve", "ILX:0794279"),
+    ("posterior A gastric branch of vagus nerve", "ILX:0794398"),
+    ("posterior B gastric branch of vagus nerve", "ILX:0794399"),
+    ("posterior C gastric branch of vagus nerve", "ILX:0794400"),
+    # ===
+    ("bronchial branch of right vagus nerve", "FMA:53613"),
+    ("superior cervical cardiac branch of right vagus nerve", "FMA:53598"),
+    ("right recurrent laryngeal nerve", "UBERON:0011767"),
+    ("extra-laryngeal branch of right recurrent laryngeal nerve to larynx", "None"),
+    ("branch of right recurrent laryngeal nerve to muscle of larynx", "None"),
+    ("oesophageal branch of right recurrent laryngeal nerve", "FMA:53608"),
+    ("tracheal branch of right recurrent laryngeal nerve", "FMA:53610"),
+    ("right inferior laryngeal nerve", "UBERON:0011767"), # same code as for left recurrent laryngeal nerve
+    ("external branch of right inferior laryngeal nerve", "None"),
+    ("anterior branch of right inferior laryngeal nerve", "None"),
+    ("posterior branch of right inferior laryngeal nerve", "None"),
+    ("communicating branch of right recurrent laryngeal nerve with superior cervical ganglion", "None"),
+    ("communicating branch of right recurrent laryngeal nerve with right internal laryngeal nerve", "FMA:53528"),
+    ("inferior cervical cardiac branch of right recurrent laryngeal nerve", "ILX:0794235"),
+    ("inferior cervical cardiac branch of right vagus nerve", "FMA:6713"),
+    ("thoracic cardiac branch of right vagus nerve", "FMA:53604"),
+    ("right cardiac branch to deep cardiac nerve plexus", "FMA:6711"),
+    ("branch of right vagus nerve to oesophageal nerve plexus", "ILX:0794299"),
+
+    # posterior vagus, a continuation of right vagus
+    ("Posterior esophageal vagus trunk", "ILX:0794858"),
+    ("Celiac branch of posterior vagal trunk", "FMA:6667"),
+    ("Greater posterior gastric nerve", "FMA:6689"),
+    ("Pyloric branch of greater posterior gastric nerve", "FMA:6677"),
+
+    # left vagus branches
+    ("left vagus nerve", "FMA:6220"),
+    ("left vagus X nerve trunk", "UBERON:0035020"),
+    ("meningeal branch of left vagus nerve", "FMA:53542"),
+    ("recurrent meningeal branch of left vagus nerve", "None"),
+    ("communicating branch of left vagus nerve with left glossopharyngeal nerve", "FMA:53560"),
+    ("auricular branch of left vagus nerve", "FMA:53535"),
+    ("communicating branch of auricular branch of left vagus nerve with left facial nerve", "FMA:53588"),
+    ("communicating branch of auricular branch of left vagus nerve with left posterior auricular nerve", "FMA:53590"),
+    ("pharyngeal branch of left vagus nerve to pharyngeal nerve plexus", "FMA:53636"),
+    ("lingual branch of left vagus nerve", "FMA:53634"),
+    ("communicating branch of pharyngeal branch of left vagus nerve with superior cervical ganglion", "None"),
+    ("branch of left vagus nerve to carotid body", "FMA:53607"),
+    ("communicating branch of superior cervical ganglion with left vagus nerve", "ILX:0794061"),
+    ("left superior laryngeal nerve", "FMA:53536"),
+    ("left internal laryngeal nerve", "FMA:53540"),
+    ("left external laryngeal nerve", "FMA:53538"),
+    ("superior branch of left internal laryngeal nerve", "FMA:53576"), # generic term???
+    ("middle branch of left internal laryngeal nerve", "None"),
+    ("inferior branch of left internal laryngeal nerve", "FMA:53582"), # generic term???
+    ("communicating branch of left internal laryngeal nerve with left recurrent laryngeal nerve", "FMA:53572"),
+    ("communicating branch of left external laryngeal nerve with left superior cardiac nerve", "FMA:53562"),
+    ("cardiopulmonary branch A of left vagus nerve", "ILX:0794160"),
+    ("cardiopulmonary branch B of left vagus nerve", "ILX:0794161"),
+    ("pulmonary branch of left vagus nerve", "FMA:6679"),
+    ("pulmonary branch A of left vagus nerve", "None"),
+    ("pulmonary branch B of left vagus nerve", "None"),
+    ("pulmonary branch C of left vagus nerve", "None"),
+    ("pulmonary branch D of left vagus nerve", "None"),
+    # === temporary branches used in the japanese dataset
+    ("left A medial pulmonary branch of vagus nerve", "ILX:0794266"),
+    ("left B medial pulmonary branch of vagus nerve", "ILX:0794267"),
+    # ===
+    ("bronchial branch of left vagus nerve", "FMA:53558"),
+    ("superior cervical cardiac branch of left vagus nerve", "FMA:53599"),
+    ("left recurrent laryngeal nerve", "UBERON:0011766"),
+    ("extra-laryngeal branch of left recurrent laryngeal nerve to larynx", "None"),
+    ("branch of left recurrent laryngeal nerve to muscle of larynx", "None"),
+    ("oesophageal branch of left recurrent laryngeal nerve", "FMA:53609"),
+    ("tracheal branch of left recurrent laryngeal nerve", "FMA:53611"),
+    ("left inferior laryngeal nerve", "UBERON:0011766"),
+    ("external branch of left inferior laryngeal nerve", "None"),
+    ("anterior branch of left inferior laryngeal nerve", "None"),
+    ("posterior branch of left inferior laryngeal nerve", "None"),
+    ("communicating branch of left recurrent laryngeal nerve with superior cervical ganglion", "None"),
+    ("communicating branch of left recurrent laryngeal nerve with left internal laryngeal nerve", "FMA:53529"),
+    ("inferior cervical cardiac branch of left recurrent laryngeal nerve", "ILX:0794244"),
+    ("inferior cervical cardiac branch of left vagus nerve", "FMA:6714"),
+    ("thoracic cardiac branch of left vagus nerve", "FMA:53605"),
+    ("left cardiac branch to deep cardiac nerve plexus", "None"),
+    ("branch of left vagus nerve to oesophageal nerve plexus", "ILX:0794310"),
+
+    # anterior vagus, a continuation of left vagus
+    ("anterior esophageal vagus trunk", "ILX:0794854"),
+    ("hepatic branch of anterior vagal trunk", "FMA:6666"),
+    ("greater anterior gastric nerve", "FMA:6684"),
+    ("branch of greater anterior gastric nerve to coeliac nerve plexus", "FMA:53675"),
+
+]
+
+def access_vagus_marker_terms():
+    return vagus_marker_terms
+
+def access_vagus_branch_terms():
+    return vagus_branch_terms
+
+# def get_vagus_branch_term(name : str):
+#     """
+#     Find term by matching name to any identifier held for a term.
+#     Raise exception if name not found.
+#     :return ( preferred name, preferred id )
+#     """
+#     for term in vagus_branch_terms:
+#         if name in term:
+#             return ( term[0], term[1] )
+#     raise NameError("Vagus annotation term '" + name + "' not found.")
+
+def get_vagus_marker_term(name : str):
+    """
+    Find term by matching name to any identifier held for a term.
+    Raise exception if name not found.
+    :return ( preferred name, preferred id )
+    """
+    for term in vagus_marker_terms:
+        if name in term:
+            return ( term[0], term[1] )
+    raise NameError("Vagus annotation term '" + name + "' not found.")
+
+def marker_name_in_terms(name : str):
+    for term in vagus_marker_terms:
+        if name in term:
+            return True
+    return False
+
+def get_vagus_branch_term(name, vagus_terms):
+    """
+    Find term by matching name to any identifier held for a term.
+    Raise exception if name not found.
+    :return ( preferred name, preferred id )
+    """
+    for term in vagus_terms:
+        if name in term:
+            return ( term[0], term[1] )
+    return ( name, "")