Add identifiers.org links when possible in resolver service (#55)

src/pyobo/apps/resolver/resolver.py

@@ -25,7 +25,7 @@
 from pyobo.apps.utils import gunicorn_option, host_option, port_option, run_app
 from pyobo.cli_utils import verbose_option
 from pyobo.constants import PYOBO_HOME
-from pyobo.identifier_utils import normalize_curie
+from pyobo.identifier_utils import get_identifiers_org_link, normalize_curie
 
 resolve_blueprint = Blueprint('resolver', __name__)
 
@@ -93,15 +93,24 @@ def _help_resolve(curie: str) -> Mapping[str, Any]:
             message='Could not identify prefix',
         )
 
+    miriam = get_identifiers_org_link(prefix, identifier)
+
     id_name_mapping = get_id_name_mapping(prefix)
     if id_name_mapping is None:
-        return dict(
+        rv = dict(
             query=curie,
             prefix=prefix,
             identifier=identifier,
             success=False,
-            message='Could not find id->name mapping for prefix',
         )
+        if miriam:
+            rv.update(dict(
+                miriam=miriam,
+                message='Could not find id->name mapping for prefix, but still able to report Identifiers.org link',
+            ))
+        else:
+            rv['message'] = 'Could not find id->name mapping for prefix'
+        return rv
 
     name = id_name_mapping.get(identifier)
     if name is None:
@@ -119,6 +128,7 @@ def _help_resolve(curie: str) -> Mapping[str, Any]:
         identifier=identifier,
         name=name,
         success=True,
+        miriam=miriam,
     )
 
 

src/pyobo/apps/resolver/templates/home.html

@@ -14,7 +14,7 @@ <h2>Ooh Na Na CURIE Resolver</h2>
                 <div class="panel-body">
                     <p>
                         This service resolves <a href="https://en.wikipedia.org/wiki/CURIE">CURIEs</a>
-                        to their labels.
+                        to their labels and builds Identifiers.org URLs when possible.
                     </p>
                     <p>
                         It has a single endpoint <code>/resolve/&lt;curie&gt;</code> that gives back JSON.
@@ -30,37 +30,42 @@ <h2>Ooh Na Na CURIE Resolver</h2>
                     </thead>
                     <tr>
                         <td><a href="{{ url_for('.resolve', curie='DOID:14330' ) }}">DOID:14330</a></td>
-                        <td>✅ exact</td>
+                        <td>🟢 exact</td>
                     </tr>
                     <tr>
                         <td><a href="{{ url_for('.resolve', curie='doid:14330' ) }}">doid:14330</a></td>
-                        <td>✅ capitalization variant</td>
+                        <td>🟢 capitalization variant</td>
                     </tr>
                     <tr>
                         <td><a href="{{ url_for('.resolve', curie='DO:14330' ) }}">DO:14330</a></td>
-                        <td>✅ synonym identified in metaregistry</td>
+                        <td>🟢 synonym identified in metaregistry</td>
                     </tr>
                     <tr>
-                        <td><a href="{{ url_for('.resolve', curie='DOID:00000' ) }}">DOID:00000</a></td>
-                        <td>❌ invalid identifier</td>
+                        <td><a href="{{ url_for('.resolve', curie='APO:0000155' ) }}">apo:0000155</a></td>
+                        <td>🟡 able to look up name, but prefix is not listed on Identifiers.org</td>
                     </tr>
                     <tr>
-                        <td><a href="{{ url_for('.resolve', curie='NNN:00000' ) }}">NNN:00000</a></td>
-                        <td>❌ invalid prefix</td>
+                        <td><a href="{{ url_for('.resolve', curie='wikidata:Q42' ) }}">wikidata:Q42</a></td>
+                        <td>🟡 able to generate Identifiers.org link, but name unavailable</td>
                     </tr>
                     <tr>
-                        <td><a href="{{ url_for('.resolve', curie='wikidata:Q42' ) }}">wikidata:Q42</a></td>
-                        <td>❌ unmapped prefix</td>
+                        <td><a href="{{ url_for('.resolve', curie='DOID:00000' ) }}">DOID:00000</a></td>
+                        <td>🔴 valid prefix, but invalid identifier</td>
+                    </tr>
+                    <tr>
+                        <td><a href="{{ url_for('.resolve', curie='NNN:00000' ) }}">NNN:00000</a></td>
+                        <td>🔴 invalid prefix</td>
                     </tr>
                 </table>
                 <div class="panel-footer">
                     <p>
-                        This service is implemented in <a href="https://github.com/pyobo/pyobo">PyOBO</a>.
-                        If you want to know more about how it was built, check this
-                        <a href="https://cthoyt.com/2020/04/18/ooh-na-na.html">blog post</a>.
+                        This service is implemented in <a href="https://github.com/pyobo/pyobo">PyOBO</a> and graciously
+                        hosted by <a href="https://envedatherapeutics.com/">Enveda Therapeutics</a>. If you want to know
+                        more about how it was built, check this <a href="https://cthoyt.com/2020/04/18/ooh-na-na.html">blog
+                        post</a>.
                     </p>
                 </div>
             </div>
         </div>
     </div>
-{% endblock %}
+{% endblock %}

src/pyobo/identifier_utils.py

@@ -2,18 +2,23 @@
 
 """Utilities for handling prefixes."""
 
+import logging
+from collections import defaultdict
+from typing import Optional, Tuple, Union
+
+from .registries import (
+    PREFIX_TO_MIRIAM_PREFIX, REMAPPINGS_PREFIX, XREF_BLACKLIST, XREF_PREFIX_BLACKLIST, XREF_SUFFIX_BLACKLIST,
+    get_miriam, get_namespace_synonyms,
+)
+
 __all__ = [
     'normalize_curie',
+    'get_identifiers_org_link',
     'normalize_prefix',
     'normalize_dashes',
 ]
 
-from collections import defaultdict
-from typing import Optional, Tuple, Union
-
-from .registries import (
-    REMAPPINGS_PREFIX, XREF_BLACKLIST, XREF_PREFIX_BLACKLIST, XREF_SUFFIX_BLACKLIST, get_namespace_synonyms,
-)
+logger = logging.getLogger(__name__)
 
 
 def alternate_strip_prefix(s, prefix):
@@ -26,6 +31,7 @@ def alternate_strip_prefix(s, prefix):
 SYNONYM_TO_KEY = get_namespace_synonyms()
 UNHANDLED_NAMESPACES = defaultdict(list)
 UBERON_UNHANDLED = defaultdict(list)
+MIRIAM = get_miriam(mappify=True)
 
 
 def normalize_prefix(prefix: str, *, curie=None, xref=None) -> Optional[str]:
@@ -79,6 +85,19 @@ def normalize_curie(node: str) -> Union[Tuple[str, str], Tuple[None, None]]:
     return norm_node_prefix, identifier
 
 
+def get_identifiers_org_link(prefix: str, identifier: str) -> Optional[str]:
+    """Get the identifiers.org URL if possible."""
+    miriam_prefix, namespace_in_lui = PREFIX_TO_MIRIAM_PREFIX.get(prefix, (None, None))
+    if not miriam_prefix and prefix in MIRIAM:
+        miriam_prefix = prefix
+        namespace_in_lui = MIRIAM[prefix]['namespaceEmbeddedInLui']
+    if not miriam_prefix:
+        return
+    if namespace_in_lui:
+        miriam_prefix = miriam_prefix.upper()
+    return f'https://identifiers.org/{miriam_prefix}:{identifier}'
+
+
 # See: https://en.wikipedia.org/wiki/Dash
 FIGURE_DASH = b'\xe2\x80\x92'.decode('utf-8')
 EN_DASH = b'\xe2\x80\x93'.decode('utf-8')

src/pyobo/registries/__init__.py

@@ -3,8 +3,8 @@
 """Extract registry information."""
 
 from .metaregistry import (  # noqa: F401
-    CURATED_REGISTRY, CURATED_URLS, NOT_AVAILABLE_AS_OBO, OBSOLETE, REMAPPINGS_PREFIX, XREF_BLACKLIST,
-    XREF_PREFIX_BLACKLIST, XREF_SUFFIX_BLACKLIST, get_curated_registry,
+    CURATED_REGISTRY, CURATED_URLS, NOT_AVAILABLE_AS_OBO, OBSOLETE, PREFIX_TO_MIRIAM_PREFIX, REMAPPINGS_PREFIX,
+    XREF_BLACKLIST, XREF_PREFIX_BLACKLIST, XREF_SUFFIX_BLACKLIST, get_curated_registry,
 )
 from .miriam import get_miriam  # noqa: F401
 from .obofoundry import get_obofoundry  # noqa: F401

src/pyobo/registries/metaregistry.json

@@ -207,6 +207,7 @@
     "doid": {
       "miriam": {
         "id": "00000233",
+        "namespaceEmbeddedInLui": true,
         "prefix": "doid"
       },
       "obofoundry": {
@@ -234,6 +235,11 @@
       "not_available_as_obo": true
     },
     "eccode": {
+      "miriam": {
+        "id": "00000004",
+        "namespaceEmbeddedInLui": false,
+        "prefix": "ec-code"
+      },
       "synonyms": [
         "EC",
         "EC-CODE",
@@ -259,6 +265,7 @@
       "download": "http://www.ebi.ac.uk/efo/efo.obo",
       "miriam": {
         "id": "00000391",
+        "namespaceEmbeddedInLui": false,
         "prefix": "efo"
       },
       "obofoundry": {
@@ -318,6 +325,11 @@
       "pattern": "\\d{7}"
     },
     "flybase": {
+      "miriam": {
+        "id": "00000030",
+        "namespaceEmbeddedInLui": false,
+        "prefix": "fb"
+      },
       "synonyms": [
         "FB",
         "FlyBase"
@@ -347,6 +359,11 @@
     },
     "go": {
       "download": "http://purl.obolibrary.org/obo/go.obo",
+      "miriam": {
+        "id": "00000022",
+        "namespaceEmbeddedInLui": true,
+        "prefix": "go"
+      },
       "synonyms": [
         "gobp",
         "gocc",
@@ -377,6 +394,7 @@
       "download": "http://purl.obolibrary.org/obo/hp.obo",
       "miriam": {
         "id": "00000571",
+        "namespaceEmbeddedInLui": true,
         "prefix": "hp"
       },
       "obofoundry": {
@@ -392,6 +410,7 @@
     "icd10": {
       "miriam": {
         "id": "00000009",
+        "namespaceEmbeddedInLui": false,
         "prefix": "icd"
       },
       "synonyms": [
@@ -504,6 +523,7 @@
     "mesh": {
       "miriam": {
         "id": "00000560",
+        "namespaceEmbeddedInLui": false,
         "prefix": "mesh"
       },
       "synonyms": [
@@ -596,6 +616,7 @@
       "download": "http://purl.obolibrary.org/obo/ncbitaxon.obo",
       "miriam": {
         "id": "00000006",
+        "namespaceEmbeddedInLui": false,
         "prefix": "taxonomy"
       },
       "pattern": "\\d+",
@@ -611,6 +632,7 @@
     "ncit": {
       "miriam": {
         "id": "00000139",
+        "namespaceEmbeddedInLui": false,
         "prefix": "ncit"
       },
       "synonyms": [
@@ -649,6 +671,7 @@
     "omit": {
       "miriam": {
         "id": "00000605",
+        "namespaceEmbeddedInLui": false,
         "prefix": "omit"
       },
       "synonyms": [
@@ -825,6 +848,7 @@
     "snomedct": {
       "miriam": {
         "id": "00000269",
+        "namespaceEmbeddedInLui": false,
         "prefix": "snomedct"
       },
       "synonyms": [
@@ -921,6 +945,7 @@
     "umls": {
       "miriam": {
         "id": "00000233",
+        "namespaceEmbeddedInLui": false,
         "prefix": "umls"
       },
       "synonyms": [

src/pyobo/registries/metaregistry.py

@@ -4,6 +4,7 @@
 
 import json
 import os
+from typing import Mapping, Tuple
 
 __all__ = [
     'CURATED_REGISTRY_PATH',
@@ -56,3 +57,9 @@ def get_curated_registry():
 REMAPPINGS_FULL = CURATED_REGISTRY['remappings']['full']
 #: Remappings for xrefs based on the prefix. Doesn't take into account the semicolon :
 REMAPPINGS_PREFIX = CURATED_REGISTRY['remappings']['prefix']
+
+PREFIX_TO_MIRIAM_PREFIX: Mapping[str, Tuple[str, str]] = {
+    prefix: (entry['miriam']['prefix'], entry['miriam']['namespaceEmbeddedInLui'])
+    for prefix, entry in CURATED_REGISTRY_DATABASE.items()
+    if 'miriam' in entry
+}

src/pyobo/registries/utils.py

@@ -33,7 +33,10 @@ def ensure_registry(
     """Download the registry (works for MIRIAM and OLS) if it doesn't already exist."""
     if not force_download and cache_path is not None and os.path.exists(cache_path):
         with open(cache_path) as file:
-            return json.load(file)
+            rv = json.load(file)
+            if mappify:
+                rv = list_to_map(rv, id_key)
+            return rv
 
     rv = _download_paginated(url, embedded_key=embedded_key)
     rv = sorted(rv, key=itemgetter(id_key))

src/pyobo/xrefdb/cli.py

@@ -11,12 +11,13 @@
 
 from .xrefs_pipeline import Canonicalizer, _iter_ooh_na_na, get_xref_df, summarize_xref_df
 from ..cli_utils import verbose_option
+from ..constants import PYOBO_HOME
 from ..identifier_utils import UNHANDLED_NAMESPACES
 
 directory_option = click.option(
     '-d', '--directory',
     type=click.Path(dir_okay=True, file_okay=False, exists=True),
-    default=os.getcwd(),
+    default=PYOBO_HOME,
 )
 
 
@@ -44,7 +45,7 @@ def _write_tsv(df: pd.DataFrame, name: str) -> None:
 
     # Export a summary dataframe
     summary_df = summarize_xref_df(xrefs_df)
-    _write_tsv(summary_df, 'inspector_javerts_xref_summary.tsv')
+    _write_tsv(summary_df, 'inspector_javerts_xrefs_summary.tsv')
 
     # Export the namespaces that haven't been handled yet
     unmapped_path = os.path.join(directory, 'inspector_javerts_unmapped_xrefs.tsv')
@@ -61,15 +62,17 @@ def ooh_na_na(directory: str):
     """Make the prefix-identifier-name dump."""
     c = Counter()
 
-    path = os.path.join(directory, 'ooh_na_na.tsv.gz')
-    with gzip.open(path, mode='wt') as gzipped_file:
+    db_path = os.path.join(directory, 'ooh_na_na.tsv.gz')
+    click.echo(f'Writing Ooh-Na-Na to {db_path}')
+    with gzip.open(db_path, mode='wt') as gzipped_file:
         print('prefix', 'identifier', 'name', sep='\t', file=gzipped_file)
         for prefix, identifier, name in _iter_ooh_na_na():
             c[prefix] += 1
             print(prefix, identifier, name, sep='\t', file=gzipped_file)
 
-    path = os.path.join(directory, 'summary.tsv')
-    with open(path, 'w') as file:
+    summary_path = os.path.join(directory, 'ooh_na_na_summary.tsv')
+    click.echo(f'Writing Ooh-Na-Na summary to {summary_path}')
+    with open(summary_path, 'w') as file:
         for k, v in c.most_common():
             print(k, v, sep='\t', file=file)