Add protein subsets used for LLM comparisons (#9)

- Upload folder using huggingface_hub (c71ff07d522312f53b66a12db16affd78be700f7)

experimental_data/llm_judge_eval/selected_caption_samples/disgenet_all_selected_proteins.tsv

@@ -0,0 +1,208 @@
+protein_id	seq_id	num_relations	annotation_score	num_pubs
+Q5T7R7	1735	2	1	2
+Q4W4Y0	2935	1	1	1
+Q96MH7	2417	1	1	4
+Q8N8I0	13742	5	2	4
+Q8WXS4	2167	4	2	2
+Q9P217	18157	4	2	2
+Q9H6B1	17435	4	2	3
+A6NEE1	11722	4	2	2
+Q15846	2911	4	2	3
+Q6UWF9	4941	3	2	4
+Q8N0W5	7257	3	2	3
+Q9ULE4	4947	2	2	3
+A6NNL0	10272	2	2	1
+A6NC05	17392	2	2	1
+Q5BKY1	8370	2	2	2
+Q96FV0	8397	2	2	2
+Q8N4S7	11074	2	2	3
+Q92623	16597	2	2	4
+Q86XI8	18160	1	2	3
+Q5T089	9228	1	2	3
+F5GYI3	16747	1	2	2
+Q6ZQN5	5432	1	2	2
+Q5JPB2	18033	1	2	3
+Q96GI7	5058	1	2	4
+Q9H0Q0	3645	1	2	5
+Q9BTA0	4923	1	2	2
+Q96EE4	2044	1	2	5
+Q8N2R8	5027	1	2	3
+Q86X40	8382	1	2	4
+Q6GMV3	12327	1	2	6
+Q5T8I3	4878	1	2	6
+Q15053	7424	1	2	3
+Q9P2W6	2751	1	2	2
+H0UI37	16558	1	2	2
+Q9NRP4	13940	1	2	4
+Q8TDY3	306	1	2	4
+A8MSI8	8569	1	2	1
+Q9NRX3	10293	1	2	2
+Q8IVF1	10271	1	2	1
+Q8N6N2	16598	1	2	3
+Q96MZ0	5769	1	2	5
+Q8TE82	13674	1	2	5
+Q86X53	4748	1	2	10
+Q5VWI1	15546	1	2	3
+Q8IZU2	17220	1	2	4
+Q96AQ2	15906	1	2	2
+Q8N0U7	1723	1	2	3
+O14603	12179	1	2	5
+Q8TD47	13344	1	2	2
+Q8NBP5	9022	1	2	4
+Q86V85	6085	1	2	5
+Q7Z5U6	17241	1	2	4
+Q6UXB0	4901	1	2	4
+Q5TGL8	12366	1	2	5
+Q3LI58	7932	1	2	2
+Q3LI63	7928	1	2	2
+Q8NA75	3759	1	2	3
+Q9Y2H5	11627	1	3	7
+Q8NGS0	10636	1	3	5
+P0C091	5473	4	3	2
+A6NMS7	8040	4	3	3
+Q9HC57	17274	2	3	4
+P61236	17415	1	3	3
+Q9UK28	16021	2	3	3
+Q4KMZ1	7249	1	3	4
+Q5VTJ3	7774	4	3	3
+Q9H939	11939	1	3	4
+Q16517	10037	2	3	6
+Q9NXP7	5881	1	3	6
+Q6ICC9	13419	2	3	5
+Q9HCE3	17843	1	3	10
+Q8NEM2	14157	2	3	13
+Q8NGU9	6069	2	3	2
+Q4KMZ8	9974	1	3	3
+Q96T17	8639	1	3	7
+Q5W0V3	5296	3	3	7
+Q8IUK8	1976	1	3	3
+Q96NA8	16529	1	3	4
+Q3KNW1	14460	1	3	1
+Q7RTS6	10866	1	3	3
+Q69YU3	648	4	3	4
+Q9HCJ5	18158	2	3	5
+Q6PK04	2048	1	3	9
+Q8NGP0	10690	6	3	4
+Q9UIG5	12180	1	3	3
+A4D0V7	3236	3	3	5
+Q9H1C7	3655	1	3	2
+Q8NE28	14999	1	3	5
+Q9Y291	13403	4	3	10
+Q63HM9	11702	1	3	3
+Q9H8G1	17785	1	3	3
+Q8IY85	4451	1	3	3
+Q9UI15	15371	1	3	3
+P43362	8669	2	3	5
+Q96KN9	3611	1	3	5
+Q3ZCW2	8174	3	3	11
+Q9UPR6	17596	1	3	4
+Q8IV03	8522	1	3	5
+Q8ND07	1382	1	3	4
+Q96QD5	3909	1	3	3
+Q0VGE8	18027	2	3	4
+Q9Y2E4	4012	3	3	7
+Q4W5P6	14271	1	3	3
+Q9H3W5	8468	1	3	3
+Q9C0I3	2243	2	3	3
+Q9H7Y0	4008	3	3	5
+Q9H8U3	17569	4	3	3
+Q9NQS1	1268	1	4	8
+Q6ZQR2	2576	1	4	5
+Q9NY57	14928	1	4	5
+Q9UF02	2163	2	4	5
+Q86UW8	6704	4	4	4
+P58166	7173	3	4	6
+Q96DY7	9398	1	4	9
+Q9HCG1	17667	3	4	6
+Q9NQE7	16555	1	4	2
+Q9BXG8	14811	2	4	5
+O60262	5708	1	4	7
+Q6NUM9	12765	1	4	8
+P49406	13052	4	4	11
+Q12796	11819	3	4	6
+Q9BUY7	4449	1	4	4
+Q8N165	11308	1	4	5
+Q9Y661	6730	1	4	3
+Q9HD64	17332	2	4	8
+Q9H0U9	16559	1	4	9
+Q717R9	3647	2	4	3
+O15090	17845	6	4	5
+Q9NYV9	15284	2	4	8
+A8MYP8	10550	1	4	2
+P31277	6818	10	4	3
+Q6ZNB6	9917	3	4	9
+Q17RF5	10543	1	4	5
+Q8N475	5514	5	4	6
+Q71RH2	15852	1	4	4
+Q9BYD1	13046	7	4	8
+Q5T1Q4	13635	2	4	5
+Q9BX82	17806	1	4	6
+Q12926	4542	2	4	8
+Q2VWP7	12174	1	4	1
+Q9ULB5	1796	4	4	3
+Q8NBF6	1270	3	4	7
+P20382	8837	4	4	5
+Q9Y5F9	11211	4	4	1
+P40313	3520	1	4	2
+Q8WW14	2745	2	4	4
+Q7Z3G6	12073	2	4	7
+Q8IX18	3989	1	4	6
+Q9BXA9	13739	5	4	5
+Q0ZLH3	11607	5	4	8
+Q641Q3	8982	3	4	5
+Q5BKT4	424	1	4	3
+Q9BQQ7	13431	3	4	5
+Q9BSG5	13408	5	4	5
+Q9HCN8	13934	4	4	8
+Q8IZU8	4269	1	4	4
+Q02338	1423	4	4	4
+Q9UKF6	3262	1	5	18
+P30989	10280	9	5	5
+P30988	1832	3	5	20
+Q96FM1	11422	2	5	11
+Q01523	3878	5	5	16
+Q99572	10923	9	5	18
+Q96J02	7350	1	5	46
+Q86TC9	9577	9	5	16
+Q8IZJ1	16941	1	5	10
+Q96IP4	15622	1	5	7
+Q00872	9574	5	5	12
+O75604	16813	1	5	9
+O94759	16461	6	5	23
+P51811	17353	4	5	9
+Q9H5J8	15348	1	5	10
+O94776	9393	2	5	26
+Q86Y07	17158	1	5	20
+Q9H936	5862	6	5	8
+P0C869	10972	1	5	5
+Q9UBP4	4045	1	5	11
+Q9NTX9	4965	1	5	5
+Q9P2K8	4369	8	5	22
+Q86W92	8256	1	5	17
+O60494	3543	7	5	19
+Q8IZD2	7863	8	5	18
+P00488	4908	8	5	24
+Q9UPY6	17201	5	5	8
+Q7Z418	7637	1	5	6
+O75175	2981	2	5	17
+O00418	4446	1	5	23
+Q15761	10166	3	5	5
+Q96SF7	15486	2	5	5
+P52566	5789	2	5	16
+Q8N960	2425	7	5	10
+P49019	6462	4	5	7
+P07492	6257	5	5	5
+O00505	7130	4	5	22
+Q1L5Z9	8327	1	5	4
+P11226	8802	4	5	23
+Q9H900	18164	1	5	11
+P54710	1199	4	5	4
+O14529	3557	9	5	7
+Q9NSY1	1508	1	5	16
+O60664	11725	1	5	21
+Q8N3V7	15174	2	5	17
+P32455	5712	1	5	26
+Q05923	4309	3	5	6
+Q9NP99	16346	3	5	16
+Q9Y2S2	3376	2	5	7
+P52564	9256	4	5	31

experimental_data/llm_judge_eval/selected_caption_samples/reactome_all_selected_proteins.tsv

@@ -0,0 +1,183 @@
+protein_id	seq_id	num_relations	annotation_score	num_pubs
+Q8TD47	13344	48	2	2
+Q6P5R6	12992	37	2	9
+A5YM69	915	8	2	3
+A8MVX0	914	8	2	2
+A1IGU5	922	8	2	1
+Q53LP3	15114	7	2	9
+Q4QY38	3736	5	2	2
+Q30KP9	3737	5	2	1
+Q30KQ7	3721	5	2	1
+P59095	14955	5	2	1
+Q6UWW0	8137	4	2	3
+Q8WUD4	2108	4	2	9
+Q6JVE5	8136	4	2	2
+Q0Z7S8	5073	4	2	0
+Q5W064	8263	3	2	2
+Q5VZ72	7378	3	2	1
+Q7Z2F6	7990	3	2	2
+B4DX44	17988	3	2	2
+A8MUZ8	17446	3	2	1
+A0A183	8129	3	2	2
+Q9Y5V0	17967	3	2	4
+Q6ZMV8	17985	3	2	1
+A8MTY0	17980	3	2	2
+B4DXR9	17986	3	2	2
+Q3LI54	7927	2	2	0
+Q3LHN1	7934	2	2	0
+A8MX34	7942	2	2	1
+A8MUX0	7918	2	2	1
+Q3LHN0	7939	2	2	0
+Q3MIV0	7935	2	2	2
+Q3LI58	7932	2	2	2
+Q3LI63	7928	2	2	2
+Q9H7T0	3527	3	3	2
+Q5SXM1	17947	3	3	2
+P59544	15298	9	3	8
+A6NDH6	10503	3	3	1
+Q96MF6	3286	4	3	4
+Q8NGQ5	10809	3	3	2
+A8MTY7	7986	2	3	1
+Q86XN6	17996	3	3	3
+Q8N349	10664	3	3	2
+P56749	2840	4	3	8
+P0C0P6	10149	8	3	4
+C9J2P7	16707	4	3	1
+D6R9N7	16709	4	3	1
+Q6IF42	10639	3	3	3
+Q8NGL1	10731	3	3	3
+Q6P3V2	17441	3	3	3
+Q8IVN8	13797	9	3	5
+Q8NGX5	10397	3	3	3
+Q9UGF6	10753	3	3	5
+Q8NH74	10379	3	3	1
+O76100	10777	3	3	3
+A6NDL8	10505	3	3	1
+P58180	10694	3	3	3
+Q8NGF4	10499	3	3	1
+Q8NGC5	10764	3	3	0
+D6R901	16712	4	3	1
+Q9HBT7	17726	3	3	2
+Q9NS67	6140	4	3	1
+Q8NG75	10752	3	3	2
+Q9NZP0	10760	3	3	2
+Q9P2D6	4906	5	3	8
+Q8N688	3728	5	3	5
+Q8N9B8	12815	4	3	4
+Q99676	17674	3	3	7
+Q96EL2	13395	6	3	9
+Q9H0M5	17963	3	3	2
+Q6V9R5	17865	3	3	2
+Q9HAH1	17859	3	3	2
+Q969M2	3582	8	3	3
+A6NH21	14026	3	3	3
+Q8NES8	3729	5	3	3
+Q9NYT6	17695	3	3	4
+Q7L945	17918	3	3	4
+Q8NH90	10497	3	3	1
+Q8NGZ6	10763	3	3	3
+A8MXZ3	7981	2	3	1
+C9JVI0	16705	4	3	1
+Q8NH40	10771	3	3	1
+Q9BR09	9874	3	3	4
+Q6UX72	1310	4	3	2
+Q02045	9530	2	4	2
+Q13106	17664	3	4	3
+Q9Y5Y3	6150	4	4	4
+Q6IV72	17781	3	4	4
+Q9UK11	17692	3	4	5
+Q8N4P2	16567	3	4	4
+Q67FW5	1311	4	4	3
+Q9Y6Q3	17584	3	4	4
+P42357	6783	3	4	7
+O14957	12400	4	4	5
+P48060	5912	7	4	5
+Q9P0J6	13065	6	4	6
+Q9BR61	205	4	4	7
+Q96L33	12920	5	4	4
+P98182	17678	3	4	3
+P57773	3588	5	4	3
+Q96MM6	6726	4	4	5
+Q96JC4	17809	3	4	1
+Q6P499	10105	2	4	5
+Q96EK7	4896	6	4	8
+Q8TCC3	13060	6	4	10
+Q9Y2C2	16983	5	4	4
+Q9BTV6	4188	4	4	7
+Q6IMI4	14933	4	4	4
+P60369	7898	2	4	4
+Q92664	15667	5	4	6
+P59540	15297	9	4	7
+Q15181	7245	6	4	12
+Q86XD5	4902	4	4	7
+Q2NL82	16546	4	4	4
+Q92914	5259	3	4	2
+Q9NQS1	1268	7	4	8
+P59533	15291	9	4	10
+P82909	7694	6	4	10
+Q9UQ72	12214	2	4	4
+Q3LI77	7916	2	4	1
+Q8N103	15369	7	4	5
+Q6X9E4	5150	7	4	4
+Q9NR77	12374	5	4	5
+Q99678	6135	4	4	3
+Q9Y5P1	10451	3	4	5
+Q8NCK3	17813	3	4	3
+P50120	12755	6	4	5
+Q96R48	10641	3	4	4
+Q6ZMV9	7745	8	4	5
+Q86Y22	3107	7	4	3
+Q8NH10	10804	3	4	0
+Q96PL1	14099	3	4	8
+O95336	59	3	4	7
+O95755	12464	7	4	4
+P16233	8268	9	5	15
+Q8WTQ1	3665	5	5	2
+P49019	6462	7	5	7
+O14796	14125	3	5	8
+Q9UPZ6	15767	9	5	9
+Q9NWX5	1059	7	5	4
+P24468	3145	2	5	13
+P41587	17094	7	5	9
+Q96HE7	4761	4	5	28
+P10301	13300	7	5	9
+O00238	1520	3	5	15
+Q8WWQ8	14940	8	5	17
+P30044	12056	9	5	18
+Q8N3Y3	8079	3	5	9
+Q6TCH7	11073	5	5	4
+O00213	812	4	5	19
+Q9UL12	13770	3	5	8
+P19256	8191	5	5	11
+Q96AX2	12465	6	5	4
+P13631	12551	10	5	13
+O14788	16144	5	5	7
+P47804	12835	7	5	4
+P08574	3623	6	5	12
+Q2T9J0	16684	3	5	3
+Q8WUP2	5135	3	5	8
+Q92847	5869	7	5	7
+P54760	4689	6	5	22
+P51606	12739	6	5	8
+P54803	5632	4	5	22
+O00567	10075	9	5	26
+Q86VX2	3101	3	5	11
+Q9Y314	10082	3	5	13
+P00326	374	8	5	10
+Q8WYH8	7166	9	5	18
+Q9Y231	5539	4	5	15
+Q9HBK9	1038	4	5	8
+Q9NSB2	8005	2	5	5
+P55327	16260	4	5	12
+Q6L8G8	7973	2	5	2
+P04264	7465	5	5	47
+P26651	16620	3	5	44
+Q8IYH5	18173	6	5	14
+Q12891	6831	5	5	7
+Q8TCT9	6616	5	5	18
+P12821	219	3	5	71
+Q9UGY1	10058	4	5	7
+Q86VE9	14027	3	5	6
+P52209	58	9	5	7
+O95528	6315	7	5	8
+Q6P3S1	3891	4	5	14

experimental_data/llm_judge_eval/selected_caption_samples/uniprot_all_selected_proteins.tsv

@@ -0,0 +1,269 @@
+protein_id	seq_id	num_relations	annotation_score	num_pubs
+P0DV60	8130	1	1	1
+C9J202	426	1	2	1
+A1IGU5	922	1	2	1
+A8MVX0	914	1	2	2
+Q7L4S7	996	1	2	3
+Q2TB18	1102	1	2	4
+A6NLC5	2025	1	2	2
+Q8WXS4	2167	1	2	2
+Q8N1D5	2539	1	2	3
+B2RV13	2559	1	2	3
+Q86WR6	2631	1	2	3
+H7C241	2854	1	2	1
+A0A1B0GTH6	3388	1	2	1
+P60606	3538	1	2	1
+A0A096LNP1	3673	1	2	1
+Q9H0Q0	3645	1	2	5
+Q4QY38	3736	1	2	2
+Q30KP9	3737	1	2	1
+Q30KQ7	3721	1	2	1
+A6NHG4	3838	1	2	2
+Q9NVM6	4033	1	2	10
+Q8N4W6	4036	1	2	2
+Q9NX36	4040	1	2	3
+P0CF75	4394	1	2	2
+Q6P2I7	4395	1	2	4
+P60002	4570	1	2	1
+Q6NSI3	5035	1	2	3
+Q6P2I3	5091	1	2	4
+Q5MNV8	5179	1	2	4
+Q8NEA4	5169	1	2	3
+Q6ZQN5	5432	1	2	2
+A0A1W2PRP0	5441	1	2	1
+P0DTW1	5625	1	2	5
+A0A0U1RQE8	5965	1	2	1
+A6NJ69	7025	1	2	1
+P0C7L1	7309	1	2	2
+Q6IE38	7303	1	2	2
+Q3LHN0	7939	1	2	0
+Q3LI62	7931	1	2	0
+Q3LI58	7932	1	2	2
+Q3LHN1	7934	1	2	0
+Q3MIV0	7935	1	2	2
+Q3LI68	7936	1	2	0
+Q3LI54	7927	1	2	0
+Q3LI63	7928	1	2	2
+Q3LI60	7930	1	2	0
+Q9UNZ5	8035	1	2	4
+Q6JVE5	8136	1	2	2
+A0A183	8129	1	2	2
+Q9Y5L5	8178	1	2	5
+Q5BKY1	8370	1	2	2
+Q8N6Q8	8969	1	2	3
+P0DMT0	9141	1	2	2
+B2RBV5	9335	1	2	3
+Q6NXP6	10368	1	2	3
+P58417	10364	1	2	4
+A0A0X1KG70	10820	1	2	1
+A0A096LPK9	10824	1	2	1
+Q9BRP1	11271	1	2	6
+A0A1W2PS18	11791	1	2	1
+B7ZBB8	11874	1	2	3
+Q9H3Y8	11920	1	2	3
+Q8IV56	12130	1	2	1
+Q8N431	12817	1	2	2
+Q5GAN4	13195	1	2	2
+Q5GAN3	13196	1	2	2
+Q6ZQQ2	13614	1	2	1
+P0C874	13615	1	2	2
+Q6ZUB0	13616	1	2	2
+Q5VYP0	13610	1	2	2
+Q5VU36	13611	1	2	1
+Q5VVP1	13612	1	2	1
+A0A286YF01	13868	1	2	2
+A0A286YFG1	13869	1	2	2
+A0A286YEY9	13862	1	2	2
+A0A286YFB4	13863	1	2	2
+A0A286YF60	13864	1	2	2
+A0A286YEV6	13865	1	2	2
+A0A286YF46	13866	1	2	2
+A0A286YF77	13867	1	2	2
+Q9NRP4	13940	1	2	4
+Q8IZQ5	13962	1	2	6
+Q96IW2	14158	1	2	2
+Q8N4L4	14681	1	2	1
+P0DTA3	14652	1	2	2
+Q5VVC0	14725	1	2	2
+A4D263	14781	1	2	4
+P59095	14955	1	2	1
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experimental_data/llm_judge_eval/selected_caption_samples/uniprotkb_proteome_UP000005640_2024_06_18.tsv.gz

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