From 3f48fd300e8d9af8dc391aa672f618d314088bdc Mon Sep 17 00:00:00 2001
From: max <max.haeussler@gmail.com>
Date: Tue, 11 Jun 2024 18:38:46 +0200
Subject: [PATCH] fixed dm

---
 graph-network/graph-network/populate.ipynb | 66 ++++++++++++++++++++--
 pyeed/core/abstractannotation.py           |  5 --
 pyeed/core/alignmentresult.py              |  5 --
 pyeed/core/blastdata.py                    |  5 --
 pyeed/core/clustalomegaresult.py           | 10 +---
 pyeed/core/dnarecord.py                    | 16 ++----
 pyeed/core/numberedsequence.py             |  5 --
 pyeed/core/organism.py                     |  5 --
 pyeed/core/pairwisealignmentresult.py      | 10 +---
 pyeed/core/proteinrecord.py                | 24 ++++----
 pyeed/core/region.py                       | 16 ++----
 pyeed/core/regionset.py                    | 14 +++--
 pyeed/core/sequence.py                     |  5 --
 pyeed/core/sequencerecord.py               | 23 ++++++--
 pyeed/core/site.py                         | 16 ++----
 pyeed/core/standardnumbering.py            |  5 --
 pyeed/fetch/ncbiproteinmapper.py           | 12 +++-
 pyeed/schemes/pyeed_schema.md              | 16 ++++--
 specifications/sequence_record.md          | 22 ++++----
 19 files changed, 150 insertions(+), 130 deletions(-)

diff --git a/graph-network/graph-network/populate.ipynb b/graph-network/graph-network/populate.ipynb
index 1f42f095..49d8066f 100644
--- a/graph-network/graph-network/populate.ipynb
+++ b/graph-network/graph-network/populate.ipynb
@@ -2,10 +2,12 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
+    "%reload_ext autoreload\n",
+    "%autoreload 2\n",
     "import json\n",
     "from pathlib import Path\n",
     "from rdflib import Graph\n",
@@ -14,6 +16,26 @@
     "from pyeed.core import ProteinRecord"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# get pyeed logger to log to file\n",
+    "import logging\n",
+    "\n",
+    "logging.getLogger(\"pyeed\").setLevel(logging.DEBUG)\n",
+    "# logger to log to file\n",
+    "logger = logging.getLogger(\"pyeed\")\n",
+    "logger.setLevel(logging.DEBUG)\n",
+    "# create file handler which logs even debug messages\n",
+    "fh = logging.FileHandler(\"pyeed.log\")\n",
+    "fh.setLevel(logging.ERROR)\n",
+    "# connect logger with file handler\n",
+    "logger.addHandler(fh)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -29,7 +51,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "1d6eff9b03b84ff99d3d478709c896ce",
+       "model_id": "ac245aa1b6714381bf5db13c78080c0d",
        "version_major": 2,
        "version_minor": 0
       },
@@ -62,6 +84,37 @@
      },
      "metadata": {},
      "output_type": "display_data"
+    },
+    {
+     "ename": "AttributeError",
+     "evalue": "'Region' object has no attribute '_repo'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[3], line 4\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mopen\u001b[39m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m../../docs/examples/ids.json\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m      2\u001b[0m     ids \u001b[38;5;241m=\u001b[39m json\u001b[38;5;241m.\u001b[39mload(f)\n\u001b[0;32m----> 4\u001b[0m seqs \u001b[38;5;241m=\u001b[39m \u001b[43mProteinRecord\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_ids\u001b[49m\u001b[43m(\u001b[49m\u001b[43mids\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/Documents/GitHub/pyeed/pyeed/core/proteinrecord.py:165\u001b[0m, in \u001b[0;36mProteinRecord.get_ids\u001b[0;34m(cls, accession_ids)\u001b[0m\n\u001b[1;32m    161\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mnest_asyncio\u001b[39;00m\n\u001b[1;32m    163\u001b[0m nest_asyncio\u001b[38;5;241m.\u001b[39mapply()\n\u001b[0;32m--> 165\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43masyncio\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    166\u001b[0m \u001b[43m    \u001b[49m\u001b[43mProteinFetcher\u001b[49m\u001b[43m(\u001b[49m\u001b[43mids\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43maccession_ids\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfetch\u001b[49m\u001b[43m(\u001b[49m\u001b[43mforce_terminal\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m    167\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/nest_asyncio.py:30\u001b[0m, in \u001b[0;36m_patch_asyncio.<locals>.run\u001b[0;34m(main, debug)\u001b[0m\n\u001b[1;32m     28\u001b[0m task \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mensure_future(main)\n\u001b[1;32m     29\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 30\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mloop\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun_until_complete\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtask\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     31\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m     32\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m task\u001b[38;5;241m.\u001b[39mdone():\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/nest_asyncio.py:98\u001b[0m, in \u001b[0;36m_patch_loop.<locals>.run_until_complete\u001b[0;34m(self, future)\u001b[0m\n\u001b[1;32m     95\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m f\u001b[38;5;241m.\u001b[39mdone():\n\u001b[1;32m     96\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m     97\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mEvent loop stopped before Future completed.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m---> 98\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/asyncio/futures.py:203\u001b[0m, in \u001b[0;36mFuture.result\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    201\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m__log_traceback \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m    202\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m--> 203\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception\u001b[38;5;241m.\u001b[39mwith_traceback(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception_tb)\n\u001b[1;32m    204\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_result\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/asyncio/tasks.py:267\u001b[0m, in \u001b[0;36mTask.__step\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m    263\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m    264\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m exc \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m    265\u001b[0m         \u001b[38;5;66;03m# We use the `send` method directly, because coroutines\u001b[39;00m\n\u001b[1;32m    266\u001b[0m         \u001b[38;5;66;03m# don't have `__iter__` and `__next__` methods.\u001b[39;00m\n\u001b[0;32m--> 267\u001b[0m         result \u001b[38;5;241m=\u001b[39m coro\u001b[38;5;241m.\u001b[39msend(\u001b[38;5;28;01mNone\u001b[39;00m)\n\u001b[1;32m    268\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    269\u001b[0m         result \u001b[38;5;241m=\u001b[39m coro\u001b[38;5;241m.\u001b[39mthrow(exc)\n",
+      "File \u001b[0;32m~/Documents/GitHub/pyeed/pyeed/fetch/proteinfetcher.py:185\u001b[0m, in \u001b[0;36mProteinFetcher.fetch\u001b[0;34m(self, **console_kwargs)\u001b[0m\n\u001b[1;32m    182\u001b[0m \u001b[38;5;66;03m# map data to objects\u001b[39;00m\n\u001b[1;32m    183\u001b[0m ncbi_responses, uniprot_response \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39midentify_data_source(responses)\n\u001b[0;32m--> 185\u001b[0m ncbi_entries \u001b[38;5;241m=\u001b[39m \u001b[43mNCBIProteinMapper\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmap\u001b[49m\u001b[43m(\u001b[49m\u001b[43mncbi_responses\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    187\u001b[0m uniprot_entries \u001b[38;5;241m=\u001b[39m [\n\u001b[1;32m    188\u001b[0m     UniprotMapper()\u001b[38;5;241m.\u001b[39mmap(\u001b[38;5;241m*\u001b[39mresp) \u001b[38;5;28;01mfor\u001b[39;00m resp \u001b[38;5;129;01min\u001b[39;00m uniprot_response\u001b[38;5;241m.\u001b[39mvalues()\n\u001b[1;32m    189\u001b[0m ]\n\u001b[1;32m    191\u001b[0m uniprot_entries\u001b[38;5;241m.\u001b[39mextend(ncbi_entries)\n",
+      "File \u001b[0;32m~/Documents/GitHub/pyeed/pyeed/fetch/ncbiproteinmapper.py:69\u001b[0m, in \u001b[0;36mNCBIProteinMapper.map\u001b[0;34m(self, responses)\u001b[0m\n\u001b[1;32m     65\u001b[0m     protein_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmap_regions(record, protein_info)\n\u001b[1;32m     67\u001b[0m     protein_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmap_sites(record, protein_info)\n\u001b[0;32m---> 69\u001b[0m     protein_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmap_cds\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrecord\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mprotein_info\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     71\u001b[0m     protein_infos\u001b[38;5;241m.\u001b[39mappend(protein_info)\n\u001b[1;32m     73\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m protein_infos\n",
+      "File \u001b[0;32m~/Documents/GitHub/pyeed/pyeed/fetch/ncbiproteinmapper.py:232\u001b[0m, in \u001b[0;36mNCBIProteinMapper.map_cds\u001b[0;34m(self, seq_record, protein_record)\u001b[0m\n\u001b[1;32m    229\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m protein_record\n\u001b[1;32m    231\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 232\u001b[0m     \u001b[43mprotein_record\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcoding_sequence\u001b[49m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_cds_regions(\n\u001b[1;32m    233\u001b[0m         cds\u001b[38;5;241m.\u001b[39mqualifiers[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcoded_by\u001b[39m\u001b[38;5;124m\"\u001b[39m][\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m    234\u001b[0m     )\n\u001b[1;32m    235\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mIndexError\u001b[39;00m:\n\u001b[1;32m    236\u001b[0m     LOGGER\u001b[38;5;241m.\u001b[39mdebug(\n\u001b[1;32m    237\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNo coding sequence reference found for \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mseq_record\u001b[38;5;241m.\u001b[39mid\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mcds\u001b[38;5;241m.\u001b[39mqualifiers\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    238\u001b[0m     )\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/sdRDM/base/datamodel.py:1048\u001b[0m, in \u001b[0;36mDataModel.__setattr__\u001b[0;34m(self, name, value)\u001b[0m\n\u001b[1;32m   1045\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_set_parent_instances(value)\n\u001b[1;32m   1046\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_check_references(name, value)\n\u001b[0;32m-> 1048\u001b[0m \u001b[38;5;28;43msuper\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__setattr__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mvalue\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m   1050\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(value, (\u001b[38;5;28mlist\u001b[39m, ListPlus)):\n\u001b[1;32m   1051\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__dict__\u001b[39m[name]\u001b[38;5;241m.\u001b[39m_parent \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/pydantic/main.py:836\u001b[0m, in \u001b[0;36mBaseModel.__setattr__\u001b[0;34m(self, name, value)\u001b[0m\n\u001b[1;32m    834\u001b[0m     attr\u001b[38;5;241m.\u001b[39m\u001b[38;5;21m__set__\u001b[39m(\u001b[38;5;28mself\u001b[39m, value)\n\u001b[1;32m    835\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel_config\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mvalidate_assignment\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m):\n\u001b[0;32m--> 836\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m__pydantic_validator__\u001b[38;5;241m.\u001b[39mvalidate_assignment(\u001b[38;5;28mself\u001b[39m, name, value)\n\u001b[1;32m    837\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel_config\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mextra\u001b[39m\u001b[38;5;124m'\u001b[39m) \u001b[38;5;241m!=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mallow\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m name \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel_fields:\n\u001b[1;32m    838\u001b[0m     \u001b[38;5;66;03m# TODO - matching error\u001b[39;00m\n\u001b[1;32m    839\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__class__\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m object has no field \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mname\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m'\u001b[39m)\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/sdRDM/base/datamodel.py:882\u001b[0m, in \u001b[0;36mDataModel._convert_extended_list_and_numpy_strings\u001b[0;34m(cls, value)\u001b[0m\n\u001b[1;32m    879\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Validator used to convert any list into a ListPlus.\"\"\"\u001b[39;00m\n\u001b[1;32m    881\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(value, \u001b[38;5;28mlist\u001b[39m):\n\u001b[0;32m--> 882\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mListPlus\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43m[\u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_convert_numpy_type\u001b[49m\u001b[43m(\u001b[49m\u001b[43mv\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mfor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mv\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mvalue\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43min_setup\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m    883\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(value, np\u001b[38;5;241m.\u001b[39mstr_):\n\u001b[1;32m    884\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mstr\u001b[39m(value)\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/sdRDM/base/listplus.py:22\u001b[0m, in \u001b[0;36mListPlus.__init__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m     19\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_attribute \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m     21\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m arg \u001b[38;5;129;01min\u001b[39;00m args:\n\u001b[0;32m---> 22\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgenerator object\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mrepr\u001b[39m(arg):\n\u001b[1;32m     23\u001b[0m         \u001b[38;5;28;01mfor\u001b[39;00m element \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mlist\u001b[39m(arg):\n\u001b[1;32m     24\u001b[0m             \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mappend(element)\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/pydantic/main.py:1006\u001b[0m, in \u001b[0;36mBaseModel.__repr__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m   1005\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__repr__\u001b[39m(\u001b[38;5;28mself\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28mstr\u001b[39m:\n\u001b[0;32m-> 1006\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m__repr_name__()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m(\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__repr_str__\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m, \u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m)\u001b[39m\u001b[38;5;124m'\u001b[39m\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/pydantic/_internal/_repr.py:55\u001b[0m, in \u001b[0;36mRepresentation.__repr_str__\u001b[0;34m(self, join_str)\u001b[0m\n\u001b[1;32m     54\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__repr_str__\u001b[39m(\u001b[38;5;28mself\u001b[39m, join_str: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28mstr\u001b[39m:\n\u001b[0;32m---> 55\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mjoin_str\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mjoin\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mrepr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mv\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43ma\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mis\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43ma\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m=\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mv\u001b[49m\u001b[38;5;132;43;01m!r}\u001b[39;49;00m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mfor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43ma\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mv\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__repr_args__\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/pydantic/_internal/_repr.py:55\u001b[0m, in \u001b[0;36m<genexpr>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m     54\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__repr_str__\u001b[39m(\u001b[38;5;28mself\u001b[39m, join_str: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28mstr\u001b[39m:\n\u001b[0;32m---> 55\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m join_str\u001b[38;5;241m.\u001b[39mjoin\u001b[43m(\u001b[49m\u001b[38;5;28;43mrepr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mv\u001b[49m\u001b[43m)\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43ma\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mis\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43ma\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m=\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mv\u001b[49m\u001b[38;5;132;43;01m!r}\u001b[39;49;00m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mfor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43ma\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mv\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01min\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__repr_args__\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/pydantic/main.py:1025\u001b[0m, in \u001b[0;36mBaseModel.__repr_args__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m   1023\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m pydantic_extra \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m   1024\u001b[0m     \u001b[38;5;28;01myield from\u001b[39;00m ((k, v) \u001b[38;5;28;01mfor\u001b[39;00m k, v \u001b[38;5;129;01min\u001b[39;00m pydantic_extra\u001b[38;5;241m.\u001b[39mitems())\n\u001b[0;32m-> 1025\u001b[0m \u001b[38;5;28;01myield from\u001b[39;00m ((k, \u001b[38;5;28mgetattr\u001b[39m(\u001b[38;5;28mself\u001b[39m, k)) \u001b[38;5;28;01mfor\u001b[39;00m k, v \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel_computed_fields\u001b[38;5;241m.\u001b[39mitems() \u001b[38;5;28;01mif\u001b[39;00m v\u001b[38;5;241m.\u001b[39mrepr)\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/pydantic/main.py:1025\u001b[0m, in \u001b[0;36m<genexpr>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m   1023\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m pydantic_extra \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m   1024\u001b[0m     \u001b[38;5;28;01myield from\u001b[39;00m ((k, v) \u001b[38;5;28;01mfor\u001b[39;00m k, v \u001b[38;5;129;01min\u001b[39;00m pydantic_extra\u001b[38;5;241m.\u001b[39mitems())\n\u001b[0;32m-> 1025\u001b[0m \u001b[38;5;28;01myield from\u001b[39;00m ((k, \u001b[38;5;28;43mgetattr\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mk\u001b[49m\u001b[43m)\u001b[49m) \u001b[38;5;28;01mfor\u001b[39;00m k, v \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmodel_computed_fields\u001b[38;5;241m.\u001b[39mitems() \u001b[38;5;28;01mif\u001b[39;00m v\u001b[38;5;241m.\u001b[39mrepr)\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/pydantic/main.py:808\u001b[0m, in \u001b[0;36mBaseModel.__getattr__\u001b[0;34m(self, item)\u001b[0m\n\u001b[1;32m    806\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    807\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__class__\u001b[39m, item):\n\u001b[0;32m--> 808\u001b[0m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43msuper\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__getattribute__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mitem\u001b[49m\u001b[43m)\u001b[49m  \u001b[38;5;66;03m# Raises AttributeError if appropriate\u001b[39;00m\n\u001b[1;32m    809\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    810\u001b[0m         \u001b[38;5;66;03m# this is the current error\u001b[39;00m\n\u001b[1;32m    811\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mAttributeError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mtype\u001b[39m(\u001b[38;5;28mself\u001b[39m)\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m object has no attribute \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mitem\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m'\u001b[39m)\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/sdRDM/base/datamodel.py:156\u001b[0m, in \u001b[0;36mDataModel.json_ld_context\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    152\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m term:\n\u001b[1;32m    153\u001b[0m         sub_annots[attr] \u001b[38;5;241m=\u001b[39m term\n\u001b[1;32m    155\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m {\n\u001b[0;32m--> 156\u001b[0m     cls_name: \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_repo\u001b[49m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mcls_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;66;03m# type: ignore\u001b[39;00m\n\u001b[1;32m    157\u001b[0m     \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39msub_annots\n\u001b[1;32m    158\u001b[0m }\n",
+      "File \u001b[0;32m~/miniconda3/envs/pyeed/lib/python3.11/site-packages/pydantic/main.py:811\u001b[0m, in \u001b[0;36mBaseModel.__getattr__\u001b[0;34m(self, item)\u001b[0m\n\u001b[1;32m    808\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28msuper\u001b[39m()\u001b[38;5;241m.\u001b[39m\u001b[38;5;21m__getattribute__\u001b[39m(item)  \u001b[38;5;66;03m# Raises AttributeError if appropriate\u001b[39;00m\n\u001b[1;32m    809\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    810\u001b[0m     \u001b[38;5;66;03m# this is the current error\u001b[39;00m\n\u001b[0;32m--> 811\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mAttributeError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mtype\u001b[39m(\u001b[38;5;28mself\u001b[39m)\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m object has no attribute \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mitem\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m'\u001b[39m)\n",
+      "\u001b[0;31mAttributeError\u001b[0m: 'Region' object has no attribute '_repo'"
+     ]
     }
    ],
    "source": [
@@ -73,10 +126,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
+    "# write json-ld files\n",
+    "for seq in seqs:\n",
+    "    with open(f\"../json/{seq.id}.json\", \"w\") as f:\n",
+    "        f.write(seq.json())\n",
+    "\n",
     "# write ttl files\n",
     "for seq in seqs:\n",
     "    g = Graph()\n",
@@ -93,7 +151,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
diff --git a/pyeed/core/abstractannotation.py b/pyeed/core/abstractannotation.py
index ec548405..34853756 100644
--- a/pyeed/core/abstractannotation.py
+++ b/pyeed/core/abstractannotation.py
@@ -47,11 +47,6 @@ class AbstractAnnotation(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/alignmentresult.py b/pyeed/core/alignmentresult.py
index 3ca642f8..d9cce044 100644
--- a/pyeed/core/alignmentresult.py
+++ b/pyeed/core/alignmentresult.py
@@ -59,11 +59,6 @@ class AlignmentResult(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/blastdata.py b/pyeed/core/blastdata.py
index f9160ccb..b024b1d5 100644
--- a/pyeed/core/blastdata.py
+++ b/pyeed/core/blastdata.py
@@ -88,11 +88,6 @@ class BlastData(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/clustalomegaresult.py b/pyeed/core/clustalomegaresult.py
index 7583ceea..13bfda76 100644
--- a/pyeed/core/clustalomegaresult.py
+++ b/pyeed/core/clustalomegaresult.py
@@ -1,16 +1,17 @@
 from typing import Dict, Optional
 from uuid import uuid4
 
-import sdRDM
 from lxml.etree import _Element
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
 
+from .alignmentresult import AlignmentResult
+
 
 class ClustalOmegaResult(
-    sdRDM.DataModel,
+    AlignmentResult,
     search_mode="unordered",
 ):
     """"""
@@ -29,11 +30,6 @@ class ClustalOmegaResult(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/dnarecord.py b/pyeed/core/dnarecord.py
index 2e284ef3..96e88757 100644
--- a/pyeed/core/dnarecord.py
+++ b/pyeed/core/dnarecord.py
@@ -1,16 +1,17 @@
-from typing import Dict, Optional, Set
+from typing import Dict, Optional
 from uuid import uuid4
 
-import sdRDM
 from lxml.etree import _Element
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
 
+from .sequencerecord import SequenceRecord
+
 
 class DNARecord(
-    sdRDM.DataModel,
+    SequenceRecord,
     search_mode="unordered",
 ):
     """A nucleic acid sequence and associated metadata 🧬"""
@@ -29,15 +30,6 @@ class DNARecord(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
-    _object_terms: Set[str] = PrivateAttr(
-        default={"http://semanticscience.org/resource/SIO_010008"}
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/numberedsequence.py b/pyeed/core/numberedsequence.py
index b82ed2de..3369ab18 100644
--- a/pyeed/core/numberedsequence.py
+++ b/pyeed/core/numberedsequence.py
@@ -38,11 +38,6 @@ class NumberedSequence(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/organism.py b/pyeed/core/organism.py
index 093386f2..fc98ca77 100644
--- a/pyeed/core/organism.py
+++ b/pyeed/core/organism.py
@@ -106,11 +106,6 @@ class Organism(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/pairwisealignmentresult.py b/pyeed/core/pairwisealignmentresult.py
index ad91298e..ed806ae3 100644
--- a/pyeed/core/pairwisealignmentresult.py
+++ b/pyeed/core/pairwisealignmentresult.py
@@ -1,16 +1,17 @@
 from typing import Dict, Optional
 from uuid import uuid4
 
-import sdRDM
 from lxml.etree import _Element
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
 
+from .alignmentresult import AlignmentResult
+
 
 class PairwiseAlignmentResult(
-    sdRDM.DataModel,
+    AlignmentResult,
     search_mode="unordered",
 ):
     """"""
@@ -57,11 +58,6 @@ class PairwiseAlignmentResult(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/proteinrecord.py b/pyeed/core/proteinrecord.py
index 6faf718f..9517e47f 100644
--- a/pyeed/core/proteinrecord.py
+++ b/pyeed/core/proteinrecord.py
@@ -1,11 +1,10 @@
 import asyncio
 import warnings
 from concurrent.futures import ThreadPoolExecutor
-from typing import Dict, List, Optional, Set
+from typing import Dict, List, Optional
 from uuid import uuid4
 
 import nest_asyncio
-import sdRDM
 from Bio.Blast import NCBIXML
 from IPython.display import clear_output
 from lxml.etree import _Element
@@ -21,10 +20,11 @@
 
 from .dnarecord import DNARecord
 from .region import Region
+from .sequencerecord import SequenceRecord
 
 
 class ProteinRecord(
-    sdRDM.DataModel,
+    SequenceRecord,
     search_mode="unordered",
 ):
     """A protein sequence and associated metadata."""
@@ -73,15 +73,6 @@ class ProteinRecord(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
-    _object_terms: Set[str] = PrivateAttr(
-        default={"http://semanticscience.org/resource/SIO_010043"}
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
@@ -100,6 +91,9 @@ def add_to_coding_sequence(
         self,
         start: Optional[int] = None,
         end: Optional[int] = None,
+        url: Optional[str] = None,
+        accession_id: Optional[str] = None,
+        name: Optional[str] = None,
         id: Optional[str] = None,
         **kwargs,
     ) -> Region:
@@ -110,11 +104,17 @@ def add_to_coding_sequence(
             id (str): Unique identifier of the 'Region' object. Defaults to 'None'.
             start (): Start position of the site.. Defaults to None
             end (): End position of the site.. Defaults to None
+            url (): URI of the annotation.. Defaults to None
+            accession_id (): Accession ID of the annotation.. Defaults to None
+            name (): A name of a sequence feature, e.g. the name of a feature. Defaults to None
         """
 
         params = {
             "start": start,
             "end": end,
+            "url": url,
+            "accession_id": accession_id,
+            "name": name,
         }
 
         if id is not None:
diff --git a/pyeed/core/region.py b/pyeed/core/region.py
index 1b195d1b..547e9224 100644
--- a/pyeed/core/region.py
+++ b/pyeed/core/region.py
@@ -1,16 +1,17 @@
-from typing import Dict, Optional, Set
+from typing import Dict, Optional
 from uuid import uuid4
 
-import sdRDM
 from lxml.etree import _Element
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
 
+from .abstractannotation import AbstractAnnotation
+
 
 class Region(
-    sdRDM.DataModel,
+    AbstractAnnotation,
     search_mode="unordered",
 ):
     """Regional annotation of a feature within a sequence. The direction of the region is defined by the start and end positions."""
@@ -40,15 +41,6 @@ class Region(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
-    _object_terms: Set[str] = PrivateAttr(
-        default={"http://semanticscience.org/resource/SIO_000370"}
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/regionset.py b/pyeed/core/regionset.py
index 3f477417..b8497be8 100644
--- a/pyeed/core/regionset.py
+++ b/pyeed/core/regionset.py
@@ -33,11 +33,6 @@ class RegionSet(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _object_terms: Set[str] = PrivateAttr(
         default={"http://semanticscience.org/resource/SIO_000370"}
     )
@@ -60,6 +55,9 @@ def add_to_regions(
         self,
         start: Optional[int] = None,
         end: Optional[int] = None,
+        url: Optional[str] = None,
+        accession_id: Optional[str] = None,
+        name: Optional[str] = None,
         id: Optional[str] = None,
         **kwargs,
     ) -> Region:
@@ -70,11 +68,17 @@ def add_to_regions(
             id (str): Unique identifier of the 'Region' object. Defaults to 'None'.
             start (): Start position of the site.. Defaults to None
             end (): End position of the site.. Defaults to None
+            url (): URI of the annotation.. Defaults to None
+            accession_id (): Accession ID of the annotation.. Defaults to None
+            name (): A name of a sequence feature, e.g. the name of a feature. Defaults to None
         """
 
         params = {
             "start": start,
             "end": end,
+            "url": url,
+            "accession_id": accession_id,
+            "name": name,
         }
 
         if id is not None:
diff --git a/pyeed/core/sequence.py b/pyeed/core/sequence.py
index 40813a82..91d85cd7 100644
--- a/pyeed/core/sequence.py
+++ b/pyeed/core/sequence.py
@@ -36,11 +36,6 @@ class Sequence(
         json_schema_extra=dict(),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/sequencerecord.py b/pyeed/core/sequencerecord.py
index 2f0a0f60..9e738ac9 100644
--- a/pyeed/core/sequencerecord.py
+++ b/pyeed/core/sequencerecord.py
@@ -101,11 +101,6 @@ class SequenceRecord(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
@@ -123,6 +118,9 @@ def _parse_raw_xml_data(self):
     def add_to_sites(
         self,
         positions: List[int] = ListPlus(),
+        url: Optional[str] = None,
+        accession_id: Optional[str] = None,
+        name: Optional[str] = None,
         id: Optional[str] = None,
         **kwargs,
     ) -> Site:
@@ -132,10 +130,16 @@ def add_to_sites(
         Args:
             id (str): Unique identifier of the 'Site' object. Defaults to 'None'.
             positions (): Position of the site(s) within the sequence.. Defaults to ListPlus()
+            url (): URI of the annotation.. Defaults to None
+            accession_id (): Accession ID of the annotation.. Defaults to None
+            name (): A name of a sequence feature, e.g. the name of a feature. Defaults to None
         """
 
         params = {
             "positions": positions,
+            "url": url,
+            "accession_id": accession_id,
+            "name": name,
         }
 
         if id is not None:
@@ -151,6 +155,9 @@ def add_to_regions(
         self,
         start: Optional[int] = None,
         end: Optional[int] = None,
+        url: Optional[str] = None,
+        accession_id: Optional[str] = None,
+        name: Optional[str] = None,
         id: Optional[str] = None,
         **kwargs,
     ) -> Region:
@@ -161,11 +168,17 @@ def add_to_regions(
             id (str): Unique identifier of the 'Region' object. Defaults to 'None'.
             start (): Start position of the site.. Defaults to None
             end (): End position of the site.. Defaults to None
+            url (): URI of the annotation.. Defaults to None
+            accession_id (): Accession ID of the annotation.. Defaults to None
+            name (): A name of a sequence feature, e.g. the name of a feature. Defaults to None
         """
 
         params = {
             "start": start,
             "end": end,
+            "url": url,
+            "accession_id": accession_id,
+            "name": name,
         }
 
         if id is not None:
diff --git a/pyeed/core/site.py b/pyeed/core/site.py
index 06b665c0..0e3d8002 100644
--- a/pyeed/core/site.py
+++ b/pyeed/core/site.py
@@ -1,16 +1,17 @@
-from typing import Dict, List, Optional, Set
+from typing import Dict, List, Optional
 from uuid import uuid4
 
-import sdRDM
 from lxml.etree import _Element
 from pydantic import PrivateAttr, model_validator
 from pydantic_xml import attr, element
 from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
 
+from .abstractannotation import AbstractAnnotation
+
 
 class Site(
-    sdRDM.DataModel,
+    AbstractAnnotation,
     search_mode="unordered",
 ):
     """Position(s) constituting a site within a sequence."""
@@ -32,15 +33,6 @@ class Site(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
-    _object_terms: Set[str] = PrivateAttr(
-        default={"http://semanticscience.org/resource/sio:010049"}
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/core/standardnumbering.py b/pyeed/core/standardnumbering.py
index e72580b9..9438ed3d 100644
--- a/pyeed/core/standardnumbering.py
+++ b/pyeed/core/standardnumbering.py
@@ -40,11 +40,6 @@ class StandardNumbering(
         ),
     )
 
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/PyEED/pyeed")
-    _commit: Optional[str] = PrivateAttr(
-        default="6cb7b2b9f86383fe9659fc93e0802306fd288462"
-    )
-
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
     @model_validator(mode="after")
diff --git a/pyeed/fetch/ncbiproteinmapper.py b/pyeed/fetch/ncbiproteinmapper.py
index dd1ebcf8..f8eef8a5 100644
--- a/pyeed/fetch/ncbiproteinmapper.py
+++ b/pyeed/fetch/ncbiproteinmapper.py
@@ -46,10 +46,13 @@ def map(self, responses: List[str]) -> List[ProteinRecord]:
 
         protein_infos = []
         for record in seq_records:
-
             protein_info = ProteinRecord(id=record.id, sequence=str(record.seq))
 
             try:
+                # print(str(record.seq))
+                # print(protein_info.sequence)
+                # print(self.map_organism(record))
+                # print(protein_info)
                 protein_info.organism = Organism(**self.map_organism(record))
             except ValidationError as e:
                 LOGGER.error(
@@ -90,13 +93,16 @@ def map_organism(self, seq_record: SeqRecord) -> dict:
                 return {}
 
             try:
-                taxonomy_id = next(feature for feature in feature.qualifiers["db_xref"] if "taxon" in feature)
+                taxonomy_id = next(
+                    feature
+                    for feature in feature.qualifiers["db_xref"]
+                    if "taxon" in feature
+                )
                 if ":" in taxonomy_id:
                     taxonomy_id = taxonomy_id.split(":")[1]
             except StopIteration:
                 taxonomy_id = None
 
-
         except KeyError:
             LOGGER.debug(f"No taxonomy ID found for {seq_record.id}: {feature}")
             return {}
diff --git a/pyeed/schemes/pyeed_schema.md b/pyeed/schemes/pyeed_schema.md
index c136922e..f21b22e9 100644
--- a/pyeed/schemes/pyeed_schema.md
+++ b/pyeed/schemes/pyeed_schema.md
@@ -1,5 +1,11 @@
 ```mermaid
 classDiagram
+    SequenceRecord <-- ProteinRecord
+    SequenceRecord <-- DNARecord
+    AbstractAnnotation <-- Site
+    AbstractAnnotation <-- Region
+    AlignmentResult <-- PairwiseAlignmentResult
+    AlignmentResult <-- ClustalOmegaResult
     SequenceRecord *-- Site
     SequenceRecord *-- Region
     SequenceRecord *-- RegionSet
@@ -67,9 +73,9 @@ classDiagram
     class BlastData {
         +float identity
         +float evalue
-        +integer n_hits
+        +int n_hits
         +string substitution_matrix
-        +integer word_size
+        +int word_size
         +float gap_open
         +float gap_extend
         +float threshold
@@ -92,12 +98,12 @@ classDiagram
         +float score
         +float identity
         +float similarity
-        +integer gaps
-        +integer mismatches
+        +int gaps
+        +int mismatches
     }
     
     class StandardNumbering {
-        +string reference_id
+        +str reference_id
         +NumberedSequence[0..*] numberd_sequences
     }
     
diff --git a/specifications/sequence_record.md b/specifications/sequence_record.md
index 775d32ab..f806b994 100644
--- a/specifications/sequence_record.md
+++ b/specifications/sequence_record.md
@@ -42,7 +42,7 @@ A molecular sequence and associated annotation data.
   - Type: RegionSet[]
   - Description: Multiple regions forming a higher order structure or feature of a sequence.
 
-### ProteinRecord (sio:SIO_010043) [SequenceRecord]
+### ProteinRecord(_SequenceRecord_) (sio:SIO_010043)
 
 A protein sequence and associated metadata.
 
@@ -63,7 +63,7 @@ A protein sequence and associated metadata.
   - Description: Calculated molecular weight of the protein based on the sequence.
   - Term: edam:data_1505
 
-### DNARecord (sio:SIO_010008) [SequenceRecord]
+### DNARecord(_SequenceRecord_) (sio:SIO_010008)
 
 A nucleic acid sequence and associated metadata 🧬
 
@@ -85,7 +85,7 @@ A nucleic acid sequence and associated metadata 🧬
   - Type: string
   - Description: A name of a sequence feature, e.g. the name of a feature
 
-### Site (sio:sio:010049) [AbstractAnnotation]
+### Site(_AbstractAnnotation_) (sio:sio:010049)
 
 Position(s) constituting a site within a sequence.
 
@@ -94,7 +94,7 @@ Position(s) constituting a site within a sequence.
   - Description: Position of the site(s) within the sequence.
   - Term: sio:SIO_000056
 
-### Region (sio:SIO_000370) [AbstractAnnotation]
+### Region(_AbstractAnnotation_) (sio:SIO_000370)
 
 Regional annotation of a feature within a sequence. The direction of the region is defined by the start and end positions.
 
@@ -169,7 +169,7 @@ Description of an organism 🦠.
   - Description: Expectation value (E) to safe hits.
   - Default: 10.0
 - n_hits
-  - Type: integer
+  - Type: int
   - Description: Number of hits to return.
   - Default: 100
 - substitution_matrix
@@ -177,7 +177,7 @@ Description of an organism 🦠.
   - Description: Substitution matrix to use.
   - Default: "BLOSUM62"
 - word_size
-  - Type: integer
+  - Type: int
   - Description: Word size of the initial match.
   - Default: 3
   - Inclusivminimum: 2
@@ -224,7 +224,7 @@ Description of an organism 🦠.
   - Type: StandardNumbering
   - Description: Standard numbering of the aligned sequences.
 
-### PairwiseAlignmentResult [AlignmentResult]
+### PairwiseAlignmentResult(_AlignmentResult_)
 
 - score
   - Type: float
@@ -236,16 +236,16 @@ Description of an organism 🦠.
   - Type: float
   - Description: Ratio of similar residues in the alignment
 - gaps
-  - Type: integer
+  - Type: int
   - Description: Number of gaps in the alignment
 - mismatches
-  - Type: integer
+  - Type: int
   - Description: Number of mismatches in the alignment
 
 ### StandardNumbering
 
 - reference_id
-  - Type: string
+  - Type: str
   - Description: Standard numbering of the reference sequence
 - numberd_sequences
   - Type: NumberedSequence[]
@@ -260,7 +260,7 @@ Description of an organism 🦠.
   - Type: string[]
   - Description: Standard numbering of the aligned sequence
 
-### ClustalOmegaResult [AlignmentResult]
+### ClustalOmegaResult(_AlignmentResult_)
 
 - version
   - Type: string