diff --git a/examples/basics/query_and_blast.ipynb b/examples/basics/query_and_blast.ipynb index d4b8d3cf..96ba2fda 100644 --- a/examples/basics/query_and_blast.ipynb +++ b/examples/basics/query_and_blast.ipynb @@ -12,6 +12,17 @@ "execution_count": 1, "metadata": {}, "outputs": [], + "source": [ + "from sdRDM.generator import generate_python_api\n", + "\n", + "generate_python_api(\"../../specifications/data_model.md\", \"../../\", \"pyEED\")" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], "source": [ "%reload_ext autoreload\n", "%autoreload 2\n", @@ -29,7 +40,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "metadata": {}, "outputs": [ { @@ -100,7 +111,10 @@ "│ │ └── \u001b[94mend\u001b[0m = 1363\n", "│ └── \u001b[94mtype\u001b[0m = coding sequence\n", "├── \u001b[94mec_number\u001b[0m = 4.1.2.13\n", - "└── \u001b[94mmol_weight\u001b[0m = 38916.0\n", + "├── \u001b[94mmol_weight\u001b[0m = 38916.0\n", + "└── \u001b[94mcitation\u001b[0m\n", + " └── \u001b[4mCitation\u001b[0m\n", + " └── \u001b[94mid\u001b[0m = citation0\n", "\n" ] } @@ -119,7 +133,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -138,7 +152,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "⬇️ Fetching protein sequences: 100%|██████████| 10/10 [00:00<00:00, 52.96it/s]" + "⬇️ Fetching protein sequences: 100%|██████████| 10/10 [00:00<00:00, 57.62it/s]" ] }, { @@ -172,7 +186,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -218,7 +232,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "metadata": {}, "outputs": [ { @@ -245,7 +259,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "metadata": {}, "outputs": [ { @@ -259,6 +273,12 @@ "├── Added table model 'ProteinInfo' to __model_meta__ table\n", "├── Model 'ProteinInfo' already registered. Skipping.\n", "├── Created table 'ProteinInfo'\n", + "├── Added table model 'ProteinInfo_citation' to __model_meta__ table\n", + "├── Created table 'ProteinInfo_citation'\n", + "├── Added table model 'Citation_authors' to __model_meta__ table\n", + "├── Created table 'Citation_authors'\n", + "├── Added table model 'ProteinInfo_substrates' to __model_meta__ table\n", + "├── Created table 'ProteinInfo_substrates'\n", "├── Added table model 'ProteinInfo_coding_sequence_ref' to __model_meta__ table\n", "├── Created table 'ProteinInfo_coding_sequence_ref'\n", "├── Added table model 'DNARegion_spans' to __model_meta__ table\n", @@ -273,12 +293,18 @@ "├── Added table model 'ProteinInfo_organism' to __model_meta__ table\n", "├── Created table 'ProteinInfo_organism'\n", "├── Added primary key 'ProteinInfo_id' to table ProteinInfo\n", + "├── Added primary key 'ProteinInfo_citation_id' to table ProteinInfo_citation\n", + "├── Added primary key 'Citation_authors_id' to table Citation_authors\n", + "├── Added primary key 'ProteinInfo_substrates_id' to table ProteinInfo_substrates\n", "├── Added primary key 'ProteinInfo_coding_sequence_ref_id' to table ProteinInfo_coding_sequence_ref\n", "├── Added primary key 'DNARegion_spans_id' to table DNARegion_spans\n", "├── Added primary key 'ProteinInfo_sites_id' to table ProteinInfo_sites\n", "├── Added primary key 'ProteinInfo_regions_id' to table ProteinInfo_regions\n", "├── Added primary key 'ProteinRegion_spans_id' to table ProteinRegion_spans\n", "├── Added primary key 'ProteinInfo_organism_id' to table ProteinInfo_organism\n", + "├── Added foreign key 'ProteinInfo_id'(ProteinInfo) to table ProteinInfo_citation\n", + "├── Added foreign key 'ProteinInfo_citation_id'(ProteinInfo_citation) to table Citation_authors\n", + "├── Added foreign key 'ProteinInfo_id'(ProteinInfo) to table ProteinInfo_substrates\n", "├── Added foreign key 'ProteinInfo_id'(ProteinInfo) to table ProteinInfo_coding_sequence_ref\n", "├── Added foreign key 'ProteinInfo_coding_sequence_ref_id'(ProteinInfo_coding_sequence_ref) to table DNARegion_spans\n", "├── Added foreign key 'ProteinInfo_id'(ProteinInfo) to table ProteinInfo_sites\n", @@ -301,24 +327,27 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['DNARegion_spans',\n", + "['Citation_authors',\n", + " 'DNARegion_spans',\n", " 'ProteinInfo',\n", + " 'ProteinInfo_citation',\n", " 'ProteinInfo_coding_sequence_ref',\n", " 'ProteinInfo_organism',\n", " 'ProteinInfo_regions',\n", " 'ProteinInfo_sites',\n", + " 'ProteinInfo_substrates',\n", " 'ProteinRegion_spans',\n", " 'Site_positions',\n", " '__model_meta__']" ] }, - "execution_count": 7, + "execution_count": 8, "metadata": {}, "output_type": "execute_result" } @@ -337,24 +366,24 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Added dataset ProteinInfo (4f426ec3-20b9-4507-b932-b08b56931bea)\n", - "Added dataset ProteinInfo (f279b756-1be7-4052-97a0-0b96e33c03d1)\n", - "Added dataset ProteinInfo (23f7184f-22e5-4c05-aba1-d078fdd489f9)\n", - "Added dataset ProteinInfo (d2eba4c6-e6ef-41d6-a0b7-263f3527988f)\n", - "Added dataset ProteinInfo (6581d172-39b2-488a-8930-661aa23c695c)\n", - "Added dataset ProteinInfo (49a9524c-ee3b-411c-b461-510739ce8f4d)\n", - "Added dataset ProteinInfo (d9c6aed7-d4b4-4a8c-b07d-b103e12e0597)\n", - "Added dataset ProteinInfo (cf180852-232f-47fd-8bb8-36de45243afc)\n", - "Added dataset ProteinInfo (e20ad027-116a-49c5-a868-9ffb4d4e563d)\n", - "Added dataset ProteinInfo (123dbc69-5043-46e6-a8ec-57780d6cfc5d)\n", - "Added dataset ProteinInfo (a931df8e-e3b0-441c-bec7-7117e801025a)\n" + "Added dataset ProteinInfo (f788c966-2df5-4393-a1f0-3dfee82fde20)\n", + "Added dataset ProteinInfo (e35241aa-bc18-4acd-b93e-9962ecb2ad32)\n", + "Added dataset ProteinInfo (3e9048bc-fac4-4ea1-8084-f592d1b8003a)\n", + "Added dataset ProteinInfo (6bfb0751-4c7c-4d6f-ac8f-6dffaad32efa)\n", + "Added dataset ProteinInfo (74fd1ced-4901-41c2-8199-f0e6b2802c17)\n", + "Added dataset ProteinInfo (04158b95-54d2-4cee-b726-0d551f4057c4)\n", + "Added dataset ProteinInfo (b865b87d-0ef9-4567-af9b-6c32817abbf1)\n", + "Added dataset ProteinInfo (1133dd16-9e23-4591-9234-3f497b844f03)\n", + "Added dataset ProteinInfo (e9251cb1-2281-407e-9664-8662c95ce449)\n", + "Added dataset ProteinInfo (0a59c085-feb5-405f-b3d4-8d1447bc2f5a)\n", + "Added dataset ProteinInfo (ff58b48a-61a0-4386-96c6-967d32b8fa21)\n" ] } ], @@ -372,63 +401,63 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 10, "metadata": {}, "outputs": [ { "data": { "text/html": [ - "
┏━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
-       "┃ name                    ┃ taxonomy_id ┃ domain    ┃ kingdom ┃ phylum     ┃ tax_class ┃ order   ┃ family        ┃ genus      ┃ species      ┃ ProteinInfo_organism_id              ┃ ProteinInfo_id                       ┃\n",
-       "┡━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
-       "│ string                  │ !string     │ string    │ string  │ string     │ string    │ string  │ string        │ string     │ string       │ !string                              │ string                               │\n",
-       "├─────────────────────────┼─────────────┼───────────┼─────────┼────────────┼───────────┼─────────┼───────────────┼────────────┼──────────────┼──────────────────────────────────────┼──────────────────────────────────────┤\n",
-       "│ Drosophila melanogaster │ taxon:7227  │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ melanogaster │ d0e04035-dba0-4b6c-9f6c-d0c994dbd27f │ 4f426ec3-20b9-4507-b932-b08b56931bea │\n",
-       "│ Drosophila melanogaster │ taxon:7227  │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ melanogaster │ bca9a960-f3c7-44fc-8d69-60f0b13bd4d3 │ f279b756-1be7-4052-97a0-0b96e33c03d1 │\n",
-       "│ Drosophila sechellia    │ taxon:7238  │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ sechellia    │ 50163d4d-8532-4fa2-9a00-1050745e2a88 │ 23f7184f-22e5-4c05-aba1-d078fdd489f9 │\n",
-       "│ Drosophila simulans     │ taxon:7240  │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ simulans     │ d90eebd0-6f72-4cd5-a4b0-21ca78bc771a │ d2eba4c6-e6ef-41d6-a0b7-263f3527988f │\n",
-       "│ Drosophila melanogaster │ taxon:7227  │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ melanogaster │ b9851da1-47f4-4a7d-b84b-db4aeb117831 │ 6581d172-39b2-488a-8930-661aa23c695c │\n",
-       "│ Drosophila erecta       │ taxon:7220  │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ erecta       │ e2f21c88-4a38-4d88-9ae6-734d31e639b3 │ 49a9524c-ee3b-411c-b461-510739ce8f4d │\n",
-       "│ Drosophila yakuba       │ taxon:7245  │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ yakuba       │ 505aa0cb-507b-4416-8611-34632d05ebd4 │ d9c6aed7-d4b4-4a8c-b07d-b103e12e0597 │\n",
-       "│ Drosophila melanogaster │ taxon:7227  │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ melanogaster │ 9a3197c7-1543-4a88-8662-69211be58db4 │ cf180852-232f-47fd-8bb8-36de45243afc │\n",
-       "│ Drosophila teissieri    │ taxon:7243  │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ teissieri    │ f0c643b7-9b8c-4675-95f6-a4e58767e021 │ e20ad027-116a-49c5-a868-9ffb4d4e563d │\n",
-       "│ Drosophila ficusphila   │ taxon:30025 │ Eukaryota │ Metazoa │ Arthropoda │ Insecta   │ Diptera │ Drosophilidae │ Drosophila │ ficusphila   │ 5f9b00b9-7e26-4124-aefd-ef3d1145a355 │ 123dbc69-5043-46e6-a8ec-57780d6cfc5d │\n",
-       "│ …                       │ …           │ …         │ …       │ …          │ …         │ …       │ …             │ …          │ …            │ …                                    │ …                                    │\n",
-       "└─────────────────────────┴─────────────┴───────────┴─────────┴────────────┴───────────┴─────────┴───────────────┴────────────┴──────────────┴──────────────────────────────────────┴──────────────────────────────────────┘\n",
+       "
┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
+       "┃ source_id      ┃ name                                        ┃ sequence                                                                         ┃ ec_number ┃ mol_weight ┃ ProteinInfo_id                       ┃\n",
+       "┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
+       "│ string         │ string                                      │ !string                                                                          │ string    │ float64    │ !string                              │\n",
+       "├────────────────┼─────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────┼───────────┼────────────┼──────────────────────────────────────┤\n",
+       "│ AEB39622.1     │ FI14722p                                    │ MTLIASEGIIAEVSVTLLSYKNIIVENYTRISKMTTYFNYPSKELQDELREIAQKIVAPGKGILAADESGPTMGKRLQD… │ NULL      │       NULL │ f788c966-2df5-4393-a1f0-3dfee82fde20 │\n",
+       "│ NP_001287541.1 │ aldolase 1, isoform M                       │ MTTYFNYPSKELQDELREIAQKIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL… │ 4.1.2.13  │    38916.0 │ e35241aa-bc18-4acd-b93e-9962ecb2ad32 │\n",
+       "│ XP_032576247.1 │ fructose-bisphosphate aldolase isoform X1   │ MTTYFNYPSKELQDELREIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL… │ NULL      │    38944.0 │ 3e9048bc-fac4-4ea1-8084-f592d1b8003a │\n",
+       "│ XP_016036385.1 │ fructose-bisphosphate aldolase isoform X1   │ MTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL… │ NULL      │    38930.0 │ 6bfb0751-4c7c-4d6f-ac8f-6dffaad32efa │\n",
+       "│ 1FBA_A         │ Chain A, FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE │ XTTYFNYPSKELQDELREIAQKIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL… │ NULL      │       NULL │ 74fd1ced-4901-41c2-8199-f0e6b2802c17 │\n",
+       "│ XP_015009248.1 │ fructose-bisphosphate aldolase isoform X3   │ MTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL… │ NULL      │    38929.0 │ 04158b95-54d2-4cee-b726-0d551f4057c4 │\n",
+       "│ XP_039231177.1 │ fructose-bisphosphate aldolase isoform X1   │ MTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL… │ NULL      │    38916.0 │ b865b87d-0ef9-4567-af9b-6c32817abbf1 │\n",
+       "│ BAA01236.1     │ aldolase gamma                              │ MTTYFNYPSKELQDELREIAQKIVAPGKGILAADESGPTHGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL… │ NULL      │       NULL │ 1133dd16-9e23-4591-9234-3f497b844f03 │\n",
+       "│ XP_043651204.1 │ fructose-bisphosphate aldolase isoform X2   │ MTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL… │ NULL      │    38930.0 │ e9251cb1-2281-407e-9664-8662c95ce449 │\n",
+       "│ XP_017052602.1 │ fructose-bisphosphate aldolase isoform X2   │ MTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL… │ NULL      │    38930.0 │ 0a59c085-feb5-405f-b3d4-8d1447bc2f5a │\n",
+       "│ …              │ …                                           │ …                                                                                │ …         │          … │ …                                    │\n",
+       "└────────────────┴─────────────────────────────────────────────┴──────────────────────────────────────────────────────────────────────────────────┴───────────┴────────────┴──────────────────────────────────────┘\n",
        "
\n"
       ],
       "text/plain": [
-       "┏━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
-       "┃\u001b[1m \u001b[0m\u001b[1mname\u001b[0m\u001b[1m                   \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mtaxonomy_id\u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mdomain\u001b[0m\u001b[1m   \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mkingdom\u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mphylum\u001b[0m\u001b[1m    \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mtax_class\u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1morder\u001b[0m\u001b[1m  \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mfamily\u001b[0m\u001b[1m       \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mgenus\u001b[0m\u001b[1m     \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mspecies\u001b[0m\u001b[1m     \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mProteinInfo_organism_id\u001b[0m\u001b[1m             \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mProteinInfo_id\u001b[0m\u001b[1m                      \u001b[0m\u001b[1m \u001b[0m┃\n",
-       "┡━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
-       "│ \u001b[2mstring\u001b[0m                  │ \u001b[2m!string\u001b[0m     │ \u001b[2mstring\u001b[0m    │ \u001b[2mstring\u001b[0m  │ \u001b[2mstring\u001b[0m     │ \u001b[2mstring\u001b[0m    │ \u001b[2mstring\u001b[0m  │ \u001b[2mstring\u001b[0m        │ \u001b[2mstring\u001b[0m     │ \u001b[2mstring\u001b[0m       │ \u001b[2m!string\u001b[0m                              │ \u001b[2mstring\u001b[0m                               │\n",
-       "├─────────────────────────┼─────────────┼───────────┼─────────┼────────────┼───────────┼─────────┼───────────────┼────────────┼──────────────┼──────────────────────────────────────┼──────────────────────────────────────┤\n",
-       "│ \u001b[32mDrosophila melanogaster\u001b[0m │ \u001b[32mtaxon:7227 \u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32mmelanogaster\u001b[0m │ \u001b[32md0e04035-dba0-4b6c-9f6c-d0c994dbd27f\u001b[0m │ \u001b[32m4f426ec3-20b9-4507-b932-b08b56931bea\u001b[0m │\n",
-       "│ \u001b[32mDrosophila melanogaster\u001b[0m │ \u001b[32mtaxon:7227 \u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32mmelanogaster\u001b[0m │ \u001b[32mbca9a960-f3c7-44fc-8d69-60f0b13bd4d3\u001b[0m │ \u001b[32mf279b756-1be7-4052-97a0-0b96e33c03d1\u001b[0m │\n",
-       "│ \u001b[32mDrosophila sechellia   \u001b[0m │ \u001b[32mtaxon:7238 \u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32msechellia   \u001b[0m │ \u001b[32m50163d4d-8532-4fa2-9a00-1050745e2a88\u001b[0m │ \u001b[32m23f7184f-22e5-4c05-aba1-d078fdd489f9\u001b[0m │\n",
-       "│ \u001b[32mDrosophila simulans    \u001b[0m │ \u001b[32mtaxon:7240 \u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32msimulans    \u001b[0m │ \u001b[32md90eebd0-6f72-4cd5-a4b0-21ca78bc771a\u001b[0m │ \u001b[32md2eba4c6-e6ef-41d6-a0b7-263f3527988f\u001b[0m │\n",
-       "│ \u001b[32mDrosophila melanogaster\u001b[0m │ \u001b[32mtaxon:7227 \u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32mmelanogaster\u001b[0m │ \u001b[32mb9851da1-47f4-4a7d-b84b-db4aeb117831\u001b[0m │ \u001b[32m6581d172-39b2-488a-8930-661aa23c695c\u001b[0m │\n",
-       "│ \u001b[32mDrosophila erecta      \u001b[0m │ \u001b[32mtaxon:7220 \u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32merecta      \u001b[0m │ \u001b[32me2f21c88-4a38-4d88-9ae6-734d31e639b3\u001b[0m │ \u001b[32m49a9524c-ee3b-411c-b461-510739ce8f4d\u001b[0m │\n",
-       "│ \u001b[32mDrosophila yakuba      \u001b[0m │ \u001b[32mtaxon:7245 \u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32myakuba      \u001b[0m │ \u001b[32m505aa0cb-507b-4416-8611-34632d05ebd4\u001b[0m │ \u001b[32md9c6aed7-d4b4-4a8c-b07d-b103e12e0597\u001b[0m │\n",
-       "│ \u001b[32mDrosophila melanogaster\u001b[0m │ \u001b[32mtaxon:7227 \u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32mmelanogaster\u001b[0m │ \u001b[32m9a3197c7-1543-4a88-8662-69211be58db4\u001b[0m │ \u001b[32mcf180852-232f-47fd-8bb8-36de45243afc\u001b[0m │\n",
-       "│ \u001b[32mDrosophila teissieri   \u001b[0m │ \u001b[32mtaxon:7243 \u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32mteissieri   \u001b[0m │ \u001b[32mf0c643b7-9b8c-4675-95f6-a4e58767e021\u001b[0m │ \u001b[32me20ad027-116a-49c5-a868-9ffb4d4e563d\u001b[0m │\n",
-       "│ \u001b[32mDrosophila ficusphila  \u001b[0m │ \u001b[32mtaxon:30025\u001b[0m │ \u001b[32mEukaryota\u001b[0m │ \u001b[32mMetazoa\u001b[0m │ \u001b[32mArthropoda\u001b[0m │ \u001b[32mInsecta  \u001b[0m │ \u001b[32mDiptera\u001b[0m │ \u001b[32mDrosophilidae\u001b[0m │ \u001b[32mDrosophila\u001b[0m │ \u001b[32mficusphila  \u001b[0m │ \u001b[32m5f9b00b9-7e26-4124-aefd-ef3d1145a355\u001b[0m │ \u001b[32m123dbc69-5043-46e6-a8ec-57780d6cfc5d\u001b[0m │\n",
-       "│ \u001b[2m…\u001b[0m                       │ \u001b[2m…\u001b[0m           │ \u001b[2m…\u001b[0m         │ \u001b[2m…\u001b[0m       │ \u001b[2m…\u001b[0m          │ \u001b[2m…\u001b[0m         │ \u001b[2m…\u001b[0m       │ \u001b[2m…\u001b[0m             │ \u001b[2m…\u001b[0m          │ \u001b[2m…\u001b[0m            │ \u001b[2m…\u001b[0m                                    │ \u001b[2m…\u001b[0m                                    │\n",
-       "└─────────────────────────┴─────────────┴───────────┴─────────┴────────────┴───────────┴─────────┴───────────────┴────────────┴──────────────┴──────────────────────────────────────┴──────────────────────────────────────┘"
+       "┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
+       "┃\u001b[1m \u001b[0m\u001b[1msource_id\u001b[0m\u001b[1m     \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mname\u001b[0m\u001b[1m                                       \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1msequence\u001b[0m\u001b[1m                                                                        \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mec_number\u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mmol_weight\u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1mProteinInfo_id\u001b[0m\u001b[1m                      \u001b[0m\u001b[1m \u001b[0m┃\n",
+       "┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
+       "│ \u001b[2mstring\u001b[0m         │ \u001b[2mstring\u001b[0m                                      │ \u001b[2m!string\u001b[0m                                                                          │ \u001b[2mstring\u001b[0m    │ \u001b[2mfloat64\u001b[0m    │ \u001b[2m!string\u001b[0m                              │\n",
+       "├────────────────┼─────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────┼───────────┼────────────┼──────────────────────────────────────┤\n",
+       "│ \u001b[32mAEB39622.1    \u001b[0m │ \u001b[32mFI14722p                                   \u001b[0m │ \u001b[32mMTLIASEGIIAEVSVTLLSYKNIIVENYTRISKMTTYFNYPSKELQDELREIAQKIVAPGKGILAADESGPTMGKRLQD…\u001b[0m │ \u001b[2mNULL\u001b[0m      │       \u001b[2mNULL\u001b[0m │ \u001b[32mf788c966-2df5-4393-a1f0-3dfee82fde20\u001b[0m │\n",
+       "│ \u001b[32mNP_001287541.1\u001b[0m │ \u001b[32maldolase 1, isoform M                      \u001b[0m │ \u001b[32mMTTYFNYPSKELQDELREIAQKIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL…\u001b[0m │ \u001b[32m4.1.2.13 \u001b[0m │    \u001b[1;36m38916.0\u001b[0m │ \u001b[32me35241aa-bc18-4acd-b93e-9962ecb2ad32\u001b[0m │\n",
+       "│ \u001b[32mXP_032576247.1\u001b[0m │ \u001b[32mfructose-bisphosphate aldolase isoform X1  \u001b[0m │ \u001b[32mMTTYFNYPSKELQDELREIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL…\u001b[0m │ \u001b[2mNULL\u001b[0m      │    \u001b[1;36m38944.0\u001b[0m │ \u001b[32m3e9048bc-fac4-4ea1-8084-f592d1b8003a\u001b[0m │\n",
+       "│ \u001b[32mXP_016036385.1\u001b[0m │ \u001b[32mfructose-bisphosphate aldolase isoform X1  \u001b[0m │ \u001b[32mMTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL…\u001b[0m │ \u001b[2mNULL\u001b[0m      │    \u001b[1;36m38930.0\u001b[0m │ \u001b[32m6bfb0751-4c7c-4d6f-ac8f-6dffaad32efa\u001b[0m │\n",
+       "│ \u001b[32m1FBA_A        \u001b[0m │ \u001b[32mChain A, FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE\u001b[0m │ \u001b[32mXTTYFNYPSKELQDELREIAQKIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL…\u001b[0m │ \u001b[2mNULL\u001b[0m      │       \u001b[2mNULL\u001b[0m │ \u001b[32m74fd1ced-4901-41c2-8199-f0e6b2802c17\u001b[0m │\n",
+       "│ \u001b[32mXP_015009248.1\u001b[0m │ \u001b[32mfructose-bisphosphate aldolase isoform X3  \u001b[0m │ \u001b[32mMTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL…\u001b[0m │ \u001b[2mNULL\u001b[0m      │    \u001b[1;36m38929.0\u001b[0m │ \u001b[32m04158b95-54d2-4cee-b726-0d551f4057c4\u001b[0m │\n",
+       "│ \u001b[32mXP_039231177.1\u001b[0m │ \u001b[32mfructose-bisphosphate aldolase isoform X1  \u001b[0m │ \u001b[32mMTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL…\u001b[0m │ \u001b[2mNULL\u001b[0m      │    \u001b[1;36m38916.0\u001b[0m │ \u001b[32mb865b87d-0ef9-4567-af9b-6c32817abbf1\u001b[0m │\n",
+       "│ \u001b[32mBAA01236.1    \u001b[0m │ \u001b[32maldolase gamma                             \u001b[0m │ \u001b[32mMTTYFNYPSKELQDELREIAQKIVAPGKGILAADESGPTHGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL…\u001b[0m │ \u001b[2mNULL\u001b[0m      │       \u001b[2mNULL\u001b[0m │ \u001b[32m1133dd16-9e23-4591-9234-3f497b844f03\u001b[0m │\n",
+       "│ \u001b[32mXP_043651204.1\u001b[0m │ \u001b[32mfructose-bisphosphate aldolase isoform X2  \u001b[0m │ \u001b[32mMTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL…\u001b[0m │ \u001b[2mNULL\u001b[0m      │    \u001b[1;36m38930.0\u001b[0m │ \u001b[32me9251cb1-2281-407e-9664-8662c95ce449\u001b[0m │\n",
+       "│ \u001b[32mXP_017052602.1\u001b[0m │ \u001b[32mfructose-bisphosphate aldolase isoform X2  \u001b[0m │ \u001b[32mMTTYFNYPSKELQDELRDIAQRIVAPGKGILAADESGPTMGKRLQDIGVENTEDNRRAYRQLLFSTDPKLAENISGVIL…\u001b[0m │ \u001b[2mNULL\u001b[0m      │    \u001b[1;36m38930.0\u001b[0m │ \u001b[32m0a59c085-feb5-405f-b3d4-8d1447bc2f5a\u001b[0m │\n",
+       "│ \u001b[2m…\u001b[0m              │ \u001b[2m…\u001b[0m                                           │ \u001b[2m…\u001b[0m                                                                                │ \u001b[2m…\u001b[0m         │          \u001b[2m…\u001b[0m │ \u001b[2m…\u001b[0m                                    │\n",
+       "└────────────────┴─────────────────────────────────────────────┴──────────────────────────────────────────────────────────────────────────────────┴───────────┴────────────┴──────────────────────────────────────┘"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "db.connection.table(\"ProteinInfo_organism\")"
+    "db.connection.table(\"ProteinInfo\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
diff --git a/examples/test.ipynb b/examples/test.ipynb
index 430fbc9b..c8af8bca 100644
--- a/examples/test.ipynb
+++ b/examples/test.ipynb
@@ -13,61 +13,63 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "aldolase = ProteinInfo.from_ncbi(\"UCS38941.1\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "JAGTRX010000119.1:1..1200\n",
-      "['JAGTRX010000119.1:1..1200']\n",
-      "\u001b[4mProteinInfo\u001b[0m\n",
-      "├── \u001b[94mid\u001b[0m = proteininfo0\n",
-      "├── \u001b[94msource_id\u001b[0m = MBS1198664.1\n",
-      "├── \u001b[94mname\u001b[0m = depolymerase family esterase\n",
-      "├── \u001b[94msequence\u001b[0m = LQDAYVYVPKNAAPAVLGGKRALMLTMHGCGQTASGNVIGTKFNWETTAEQYGMVVVAPTVPSGTTSTRSVSGCWDWFGSAHTRTGRDAVPLKKLLDSVKARTNLDIDPNQIYVTGLSSGGGETIVMGCSFPEYFAGVGINAGPALGSASGDISVEPKVTAAQVASYCKAAATSTYTPYFATQITNAVYGTSDYLVKPNHNVRNIQGMAVVYGMTMGTPVTSSVAGGGTAKVYKDANGKERLSDLAVTGMGHAWPAGGGAGAAYVDTSHVNFPVYITKWFFDNNLRVSGGSTTTTTAATTTTTGGATTTTGAATTTTAAATTTTTRASTTTTTTTTTTTAGACYKTSNYAHVTAGRAYNSLGTAKAKGSNQSMGLNNTFYITKLRMTGTAYYVIDATCP\n",
-      "├── \u001b[94morganism\u001b[0m\n",
-      "│   └── \u001b[4mOrganism\u001b[0m\n",
-      "│       ├── \u001b[94mid\u001b[0m = organism3\n",
-      "│       ├── \u001b[94mname\u001b[0m = Pseudomonadota bacterium\n",
-      "│       ├── \u001b[94mtaxonomy_id\u001b[0m = taxon:1977087\n",
-      "│       ├── \u001b[94mdomain\u001b[0m = Bacteria\n",
-      "│       ├── \u001b[94mkingdom\u001b[0m = Pseudomonadota\n",
-      "│       └── \u001b[94mspecies\u001b[0m = bacterium\n",
-      "└── \u001b[94mcoding_sequence_ref\u001b[0m\n",
-      "    └── \u001b[4mDNARegion\u001b[0m\n",
-      "        ├── \u001b[94mid\u001b[0m = JAGTRX010000119.1\n",
-      "        ├── \u001b[94mspans\u001b[0m\n",
-      "        │   └── 0\n",
-      "        │       └── \u001b[4mSpan\u001b[0m\n",
-      "        │           ├── \u001b[94mid\u001b[0m = span0\n",
-      "        │           ├── \u001b[94mstart\u001b[0m = 1\n",
-      "        │           └── \u001b[94mend\u001b[0m = 1200\n",
-      "        └── \u001b[94mtype\u001b[0m = coding sequence\n",
-      "\n"
-     ]
+     "data": {
+      "text/plain": [
+       "Substrate(id='substrate0', name='GAPDH', inchi=None, smiles=None, chebi_id=None)"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
-    "aldolase = ProteinInfo.from_ncbi(\"MBS1198664.1\")\n",
-    "print(aldolase)"
+    "aldolase.add_to_substrates(\"GAPDH\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
-     "ename": "AttributeError",
-     "evalue": "'NoneType' object has no attribute 'pblast'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
-      "\u001b[1;32m/Users/max/Documents/GitHub/pyeed/examples/test.ipynb Cell 3\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> 1\u001b[0m blast_results \u001b[39m=\u001b[39m aldolase\u001b[39m.\u001b[39;49mpblast(n_hits\u001b[39m=\u001b[39m\u001b[39m50\u001b[39m, e_value\u001b[39m=\u001b[39m\u001b[39m1e-50\u001b[39m)\n",
-      "\u001b[0;31mAttributeError\u001b[0m: 'NoneType' object has no attribute 'pblast'"
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "🏃🏼‍♀️ Running PBLAST\n",
+      "╭── protein name: TEM1\n",
+      "├── accession: UCS38941.1\n",
+      "├── organism: Nakaseomyces glabratus\n",
+      "├── e-value: 1e-50\n",
+      "╰── max hits: 50\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "⬇️ Fetching protein sequences: 100%|██████████| 50/50 [00:04<00:00, 11.25it/s]\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "🎉 Done\n",
+      "\n"
      ]
     }
    ],
diff --git a/poetry.lock b/poetry.lock
index 8f2e22e2..cbdb7af3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,111 +2,99 @@
 
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+    {file = "aiohttp-3.9.1.tar.gz", hash = "sha256:8fc49a87ac269d4529da45871e2ffb6874e87779c3d0e2ccd813c0899221239d"},
 ]
 
 [package.dependencies]
 aiosignal = ">=1.1.2"
-async-timeout = ">=4.0.0a3,<5.0"
+async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
-charset-normalizer = ">=2.0,<4.0"
 frozenlist = ">=1.1.1"
 multidict = ">=4.5,<7.0"
 yarl = ">=1.0,<2.0"
 
 [package.extras]
-speedups = ["Brotli", "aiodns", "cchardet"]
+speedups = ["Brotli", "aiodns", "brotlicffi"]
 
 [[package]]
 name = "aiosignal"
@@ -124,13 +112,13 @@ frozenlist = ">=1.1.0"
 
 [[package]]
 name = "anytree"
-version = "2.12.0"
+version = "2.12.1"
 description = "Powerful and Lightweight Python Tree Data Structure with various plugins"
 optional = false
 python-versions = ">=3.7.2,<4"
 files = [
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+    {file = "anytree-2.12.1.tar.gz", hash = "sha256:244def434ccf31b668ed282954e5d315b4e066c4940b94aff4a7962d85947830"},
 ]
 
 [package.dependencies]
@@ -285,13 +273,13 @@ test = ["hypothesis", "pytest", "pytest-benchmark[histogram]", "pytest-cov", "py
 
 [[package]]
 name = "bigtree"
-version = "0.14.4"
+version = "0.14.5"
 description = "Tree Implementation and Methods for Python, integrated with Python list, dictionary, and pandas DataFrame."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "bigtree-0.14.5.tar.gz", hash = "sha256:29aa9cbd8c6c0ee1708634929030e136b1d84bd3e4c656bdcdb0b0dc53f9706f"},
 ]
 
 [package.extras]
@@ -337,29 +325,29 @@ numpy = "*"
 
 [[package]]
 name = "black"
-version = "23.10.1"
+version = "23.11.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "black-23.11.0.tar.gz", hash = "sha256:4c68855825ff432d197229846f971bc4d6666ce90492e5b02013bcaca4d9ab05"},
 ]
 
 [package.dependencies]
@@ -390,13 +378,13 @@ files = [
 
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
-    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
+    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
+    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
 ]
 
 [[package]]
@@ -581,13 +569,13 @@ idna = ">=2.0.0"
 
 [[package]]
 name = "fastjsonschema"
-version = "2.18.1"
+version = "2.19.0"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 files = [
-    {file = "fastjsonschema-2.18.1-py3-none-any.whl", hash = "sha256:aec6a19e9f66e9810ab371cc913ad5f4e9e479b63a7072a2cd060a9369e329a8"},
-    {file = "fastjsonschema-2.18.1.tar.gz", hash = "sha256:06dc8680d937628e993fa0cd278f196d20449a1adc087640710846b324d422ea"},
+    {file = "fastjsonschema-2.19.0-py3-none-any.whl", hash = "sha256:b9fd1a2dd6971dbc7fee280a95bd199ae0dd9ce22beb91cc75e9c1c528a5170e"},
+    {file = "fastjsonschema-2.19.0.tar.gz", hash = "sha256:e25df6647e1bc4a26070b700897b07b542ec898dd4f1f6ea013e7f6a88417225"},
 ]
 
 [package.extras]
@@ -771,13 +759,13 @@ test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre
 
 [[package]]
 name = "google-api-core"
-version = "2.12.0"
+version = "2.14.0"
 description = "Google API client core library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-core-2.12.0.tar.gz", hash = "sha256:c22e01b1e3c4dcd90998494879612c38d0a3411d1f7b679eb89e2abe3ce1f553"},
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+    {file = "google-api-core-2.14.0.tar.gz", hash = "sha256:5368a4502b793d9bbf812a5912e13e4e69f9bd87f6efb508460c43f5bbd1ce41"},
+    {file = "google_api_core-2.14.0-py3-none-any.whl", hash = "sha256:de2fb50ed34d47ddbb2bd2dcf680ee8fead46279f4ed6b16de362aca23a18952"},
 ]
 
 [package.dependencies]
@@ -1070,13 +1058,13 @@ test = ["objgraph", "psutil"]
 
 [[package]]
 name = "humanize"
-version = "4.8.0"
+version = "4.9.0"
 description = "Python humanize utilities"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "humanize-4.8.0-py3-none-any.whl", hash = "sha256:8bc9e2bb9315e61ec06bf690151ae35aeb65651ab091266941edf97c90836404"},
-    {file = "humanize-4.8.0.tar.gz", hash = "sha256:9783373bf1eec713a770ecaa7c2d7a7902c98398009dfa3d8a2df91eec9311e8"},
+    {file = "humanize-4.9.0-py3-none-any.whl", hash = "sha256:ce284a76d5b1377fd8836733b983bfb0b76f1aa1c090de2566fcf008d7f6ab16"},
+    {file = "humanize-4.9.0.tar.gz", hash = "sha256:582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa"},
 ]
 
 [package.extras]
@@ -1084,13 +1072,13 @@ tests = ["freezegun", "pytest", "pytest-cov"]
 
 [[package]]
 name = "ibis-framework"
-version = "7.0.0"
+version = "7.1.0"
 description = "Productivity-centric Python Big Data Framework"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
-    {file = "ibis_framework-7.0.0-py3-none-any.whl", hash = "sha256:d9148dc6ce737ab1715b36e99a4aaadcfd0bc8762965416dbd2fd1e7465702dc"},
-    {file = "ibis_framework-7.0.0.tar.gz", hash = "sha256:6b0aa21e7534465252acee85e2cd2b51de1b8efa5f7a52fd5389e1c960a1ea11"},
+    {file = "ibis_framework-7.1.0-py3-none-any.whl", hash = "sha256:5ef8c0204c00002c80010cd78627cd446c7a2630126a61640989c38890ffb1ad"},
+    {file = "ibis_framework-7.1.0.tar.gz", hash = "sha256:2eceb8c461230550dea43db8efd5c3ecb066a063fc0ef59e25450053eb412900"},
 ]
 
 [package.dependencies]
@@ -1101,51 +1089,52 @@ multipledispatch = ">=0.6,<2"
 numpy = ">=1,<2"
 pandas = ">=1.2.5,<3"
 parsy = ">=2,<3"
-pins = {version = ">=0.8.2,<1", extras = ["gcs"]}
-pyarrow = ">=2,<14"
+pins = {version = ">=0.8.3,<1", extras = ["gcs"]}
+pyarrow = ">=2,<15"
+pyarrow-hotfix = ">=0.4,<1"
 pymysql = {version = ">=1,<2", optional = true, markers = "extra == \"all\" or extra == \"mysql\""}
 python-dateutil = ">=2.8.2,<3"
 pytz = ">=2022.7"
 rich = ">=12.4.4,<14"
 sqlalchemy = {version = ">=1.4,<3", optional = true, markers = "extra == \"all\" or extra == \"clickhouse\" or extra == \"druid\" or extra == \"duckdb\" or extra == \"impala\" or extra == \"mssql\" or extra == \"mysql\" or extra == \"oracle\" or extra == \"postgres\" or extra == \"pyspark\" or extra == \"sqlite\" or extra == \"trino\""}
 sqlalchemy-views = {version = ">=0.3.1,<1", optional = true, markers = "extra == \"all\" or extra == \"duckdb\" or extra == \"mssql\" or extra == \"mysql\" or extra == \"oracle\" or extra == \"postgres\" or extra == \"snowflake\" or extra == \"sqlite\" or extra == \"trino\""}
-sqlglot = ">=18.7.0,<19"
+sqlglot = ">=18.12.0,<20"
 toolz = ">=0.11,<1"
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 [package.dependencies]
 numpy = ">=1.16.6"
 
+[[package]]
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+version = "0.6"
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 description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)"
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 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
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 ]
 
 [[package]]
@@ -2055,17 +2066,18 @@ files = [
 
 [[package]]
 name = "pygments"
-version = "2.16.1"
+version = "2.17.2"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
 plugins = ["importlib-metadata"]
+windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pymysql"
@@ -2208,13 +2220,13 @@ notebook = ["pygments"]
 
 [[package]]
 name = "referencing"
-version = "0.30.2"
+version = "0.31.0"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -2280,110 +2292,110 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "rpds-py"
-version = "0.12.0"
+version = "0.13.1"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
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+    {file = "yarl-1.9.3.tar.gz", hash = "sha256:4a14907b597ec55740f63e52d7fee0e9ee09d5b9d57a4f399a7423268e457b57"},
 ]
 
 [package.dependencies]
diff --git a/pyEED/core/__init__.py b/pyEED/core/__init__.py
index 99733a21..cba21b64 100644
--- a/pyEED/core/__init__.py
+++ b/pyEED/core/__init__.py
@@ -1,6 +1,9 @@
 from .proteininfo import ProteinInfo
 from .dnainfo import DNAInfo
 from .abstractregion import AbstractRegion
+from .citation import Citation
+from .author import Author
+from .substrate import Substrate
 from .dnaregion import DNARegion
 from .proteinregion import ProteinRegion
 from .span import Span
@@ -16,6 +19,9 @@
     "ProteinInfo",
     "DNAInfo",
     "AbstractRegion",
+    "Citation",
+    "Author",
+    "Substrate",
     "DNARegion",
     "ProteinRegion",
     "Span",
diff --git a/pyEED/core/author.py b/pyEED/core/author.py
new file mode 100644
index 00000000..133f2933
--- /dev/null
+++ b/pyEED/core/author.py
@@ -0,0 +1,26 @@
+import sdRDM
+
+from typing import Optional
+from pydantic import Field
+from sdRDM.base.utils import forge_signature, IDGenerator
+
+
+@forge_signature
+class Author(sdRDM.DataModel):
+    """"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("authorINDEX"),
+        xml="@id",
+    )
+
+    given_name: Optional[str] = Field(
+        default=None,
+        description="Given name of the author",
+    )
+
+    family_name: Optional[str] = Field(
+        default=None,
+        description="Family name of the author",
+    )
diff --git a/pyEED/core/citation.py b/pyEED/core/citation.py
new file mode 100644
index 00000000..fa01c2b5
--- /dev/null
+++ b/pyEED/core/citation.py
@@ -0,0 +1,64 @@
+import sdRDM
+
+from typing import List, Optional
+from pydantic import Field
+from sdRDM.base.listplus import ListPlus
+from sdRDM.base.utils import forge_signature, IDGenerator
+from .author import Author
+
+
+@forge_signature
+class Citation(sdRDM.DataModel):
+    """Information on publication of the entry 📖"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("citationINDEX"),
+        xml="@id",
+    )
+
+    doi: Optional[str] = Field(
+        default=None,
+        description="DOI of the publication",
+    )
+
+    pubmed_id: Optional[str] = Field(
+        default=None,
+        description="PubMed ID of the publication",
+    )
+
+    medline_id: Optional[str] = Field(
+        default=None,
+        description="Medline ID of the publication",
+    )
+
+    year: Optional[int] = Field(
+        default=None,
+        description="Year of publication",
+    )
+
+    authors: List[Author] = Field(
+        description="Authors of the publication",
+        default_factory=ListPlus,
+        multiple=True,
+    )
+
+    def add_to_authors(
+        self,
+        given_name: Optional[str] = None,
+        family_name: Optional[str] = None,
+        id: Optional[str] = None,
+    ) -> None:
+        """
+        This method adds an object of type 'Author' to attribute authors
+
+        Args:
+            id (str): Unique identifier of the 'Author' object. Defaults to 'None'.
+            given_name (): Given name of the author. Defaults to None
+            family_name (): Family name of the author. Defaults to None
+        """
+        params = {"given_name": given_name, "family_name": family_name}
+        if id is not None:
+            params["id"] = id
+        self.authors.append(Author(**params))
+        return self.authors[-1]
diff --git a/pyEED/core/dnainfo.py b/pyEED/core/dnainfo.py
index 0ed3dc93..a284c9aa 100644
--- a/pyEED/core/dnainfo.py
+++ b/pyEED/core/dnainfo.py
@@ -4,10 +4,10 @@
 from pydantic import Field
 from sdRDM.base.listplus import ListPlus
 from sdRDM.base.utils import forge_signature, IDGenerator
-from .organism import Organism
-from .dnaregiontype import DNARegionType
 from .dnaregion import DNARegion
 from .span import Span
+from .organism import Organism
+from .dnaregiontype import DNARegionType
 from ..ncbi.seq_io import get_ncbi_entry, _seqio_to_dna_info
 
 
diff --git a/pyEED/core/dnaregion.py b/pyEED/core/dnaregion.py
index 63f0925c..db533d00 100644
--- a/pyEED/core/dnaregion.py
+++ b/pyEED/core/dnaregion.py
@@ -2,8 +2,8 @@
 from typing import Optional
 from pydantic import Field
 from sdRDM.base.utils import forge_signature, IDGenerator
-from .dnaregiontype import DNARegionType
 from .abstractregion import AbstractRegion
+from .dnaregiontype import DNARegionType
 
 
 @forge_signature
diff --git a/pyEED/core/proteininfo.py b/pyEED/core/proteininfo.py
index 40e41f23..3a18997d 100644
--- a/pyEED/core/proteininfo.py
+++ b/pyEED/core/proteininfo.py
@@ -6,13 +6,15 @@
 from sdRDM.base.utils import forge_signature, IDGenerator
 from Bio.Blast import NCBIWWW, NCBIXML
 from pyEED.core.dnainfo import DNAInfo
-from .site import Site
+from .dnaregion import DNARegion
 from .proteinsitetype import ProteinSiteType
-from .organism import Organism
 from .proteinregion import ProteinRegion
-from .dnaregion import DNARegion
 from .span import Span
+from .citation import Citation
+from .substrate import Substrate
+from .organism import Organism
 from .proteinregiontype import ProteinRegionType
+from .site import Site
 from ..ncbi.seq_io import _seqio_to_nucleotide_info, get_ncbi_entry, get_ncbi_entrys
 
 
@@ -59,8 +61,8 @@ class ProteinInfo(sdRDM.DataModel):
     )
 
     coding_sequence_ref: Optional[DNARegion] = Field(
-        default=DNARegion(),
         description="Defines the coding sequence of the protein",
+        default_factory=DNARegion,
     )
 
     ec_number: Optional[str] = Field(
@@ -73,6 +75,17 @@ class ProteinInfo(sdRDM.DataModel):
         description="Calculated molecular weight of the protein",
     )
 
+    substrates: List[Substrate] = Field(
+        description="Promiscuous substrates of the protein",
+        default_factory=ListPlus,
+        multiple=True,
+    )
+
+    citation: Optional[Citation] = Field(
+        description="Publication on the protein",
+        default_factory=Citation,
+    )
+
     def add_to_regions(
         self,
         type: Optional[ProteinRegionType] = None,
@@ -134,6 +147,30 @@ def add_to_sites(
         self.sites.append(Site(**params))
         return self.sites[-1]
 
+    def add_to_substrates(
+        self,
+        name: Optional[str] = None,
+        inchi: Optional[str] = None,
+        smiles: Optional[str] = None,
+        chebi_id: Optional[str] = None,
+        id: Optional[str] = None,
+    ) -> None:
+        """
+        This method adds an object of type 'Substrate' to attribute substrates
+
+        Args:
+            id (str): Unique identifier of the 'Substrate' object. Defaults to 'None'.
+            name (): Name of the substrate. Defaults to None
+            inchi (): InChI code of the substrate. Defaults to None
+            smiles (): SMILES code of the substrate. Defaults to None
+            chebi_id (): ChEBI ID of the substrate. Defaults to None
+        """
+        params = {"name": name, "inchi": inchi, "smiles": smiles, "chebi_id": chebi_id}
+        if id is not None:
+            params["id"] = id
+        self.substrates.append(Substrate(**params))
+        return self.substrates[-1]
+
     @classmethod
     def from_ncbi(cls, accession_id: str) -> "ProteinInfo":
         """
diff --git a/pyEED/core/substrate.py b/pyEED/core/substrate.py
new file mode 100644
index 00000000..33339482
--- /dev/null
+++ b/pyEED/core/substrate.py
@@ -0,0 +1,36 @@
+import sdRDM
+
+from typing import Optional
+from pydantic import Field
+from sdRDM.base.utils import forge_signature, IDGenerator
+
+
+@forge_signature
+class Substrate(sdRDM.DataModel):
+    """Promiscuous substrate of an enzyme 🧪"""
+
+    id: Optional[str] = Field(
+        description="Unique identifier of the given object.",
+        default_factory=IDGenerator("substrateINDEX"),
+        xml="@id",
+    )
+
+    name: Optional[str] = Field(
+        default=None,
+        description="Name of the substrate",
+    )
+
+    inchi: Optional[str] = Field(
+        default=None,
+        description="InChI code of the substrate",
+    )
+
+    smiles: Optional[str] = Field(
+        default=None,
+        description="SMILES code of the substrate",
+    )
+
+    chebi_id: Optional[str] = Field(
+        default=None,
+        description="ChEBI ID of the substrate",
+    )
diff --git a/pyEED/ncbi/seq_io.py b/pyEED/ncbi/seq_io.py
index 2b1361d2..7350853a 100644
--- a/pyEED/ncbi/seq_io.py
+++ b/pyEED/ncbi/seq_io.py
@@ -1,10 +1,10 @@
 import re
 import secrets
-import time
+from datetime import datetime
 from tqdm import tqdm
 from typing import List
 from Bio import SeqIO, Entrez
-from Bio.SeqFeature import FeatureLocation, CompoundLocation
+from pyEED.core.citation import Citation
 from pyEED.core.dnaregion import DNARegion
 from pyEED.core.dnaregiontype import DNARegionType
 from pyEED.core.proteinregion import ProteinRegion
diff --git a/pyEED/schemes/pyeed_schema.md b/pyEED/schemes/pyeed_schema.md
index e417ec5e..4879c58b 100644
--- a/pyEED/schemes/pyeed_schema.md
+++ b/pyEED/schemes/pyeed_schema.md
@@ -2,6 +2,8 @@
 classDiagram
     AbstractRegion <-- DNARegion
     AbstractRegion <-- ProteinRegion
+    ProteinInfo *-- Citation
+    ProteinInfo *-- Substrate
     ProteinInfo *-- DNARegion
     ProteinInfo *-- ProteinRegion
     ProteinInfo *-- Site
@@ -9,6 +11,7 @@ classDiagram
     DNAInfo *-- DNARegion
     DNAInfo *-- Organism
     AbstractRegion *-- Span
+    Citation *-- Author
     DNARegion *-- DNARegionType
     ProteinRegion *-- ProteinRegionType
     Site *-- ProteinSiteType
@@ -24,6 +27,8 @@ classDiagram
         +DNARegion coding_sequence_ref
         +string ec_number
         +float mol_weight
+        +Substrate[0..*] substrates
+        +Citation citation
     }
     
     class DNAInfo {
@@ -41,6 +46,26 @@ classDiagram
         +string cross_reference
     }
     
+    class Citation {
+        +str doi
+        +str pubmed_id
+        +str medline_id
+        +int year
+        +Author[0..*] authors
+    }
+    
+    class Author {
+        +str given_name
+        +str family_name
+    }
+    
+    class Substrate {
+        +str name
+        +str inchi
+        +str smiles
+        +str chebi_id
+    }
+    
     class DNARegion {
         +DNARegionType type
     }
diff --git a/specifications/data_model.md b/specifications/data_model.md
index f62e17d4..c476c9ac 100644
--- a/specifications/data_model.md
+++ b/specifications/data_model.md
@@ -38,9 +38,17 @@ Description of a protein sequence. Additionally, the `ProteinSequence` contains
 - mol_weight
   - Type: float
   - Description: Calculated molecular weight of the protein
+- substrates
+  - Type: [Substrate](#Substrate)
+  - Description: Promiscuous substrates of the protein
+  - Multiple: True
+- citation
+  - Type: [Citation](#Citation)
+  - Description: Publication on the protein
 
 
 
+
 ### DNAInfo
 
 Description of a nucleotide sequence 🧬
@@ -92,6 +100,68 @@ Annotation of a region within a sequence 🗺️
 
 
 
+### Citation
+
+Information on publication of the entry 📖
+
+

+  Inspect attributes
+
+- doi
+  - Type: str
+  - Description: DOI of the publication
+- pubmed_id
+  - Type: str
+  - Description: PubMed ID of the publication
+- medline_id
+  - Type: str
+  - Description: Medline ID of the publication
+- year
+  - Type: int
+  - Description: Year of publication
+- authors
+  - Type: Author
+  - Description: Authors of the publication
+  - Multiple: True
+
+

+
+### Author
+
+

+  Inspect attributes
+
+- given_name
+  - Type: str
+  - Description: Given name of the author
+- family_name
+  - Type: str
+  - Description: Family name of the author
+
+

+
+### Substrate
+
+Promiscuous substrate of an enzyme 🧪
+
+

+  Inspect attributes
+
+- name
+  - Type: str
+  - Description: Name of the substrate
+- inchi
+  - Type: str
+  - Description: InChI code of the substrate
+- smiles
+  - Type: str
+  - Description: SMILES code of the substrate
+- chebi_id
+  - Type: str
+  - Description: ChEBI ID of the substrate
+
+

+
 ### DNARegion[_AbstractRegion_]
 
 - type