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levitsky / pyteomics

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.
http://pyteomics.readthedocs.io
Apache License 2.0
105 stars 34 forks source link

Problems with loading Unimod into PostgreSQL #47

Open radusuciu opened 3 years ago

radusuciu commented 3 years ago

Hi, thanks for the great project. I'm attempting to load the latest Unimod XML file into Postgres using pyteomics and have encountered a few errors that I've attempted to solve along the way. I've documented the process I've undertaken as best I could but please let me know if you'd like more information, or if I've made a mistake along the way.

I'm attempting to load data into a PostgreSQL 12 database like so:

from pyteomics.mass import unimod

unimod.load(
    'unimod_tables.xml',
    output_path='postgresql://unimod:unimod@localhost:5432/unimod'
)

This database lives in a docker container, brought up with docker-compose:

version: '3.8'

services:
    postgres:
        image: postgres:12
        environment:
            POSTGRES_PASSWORD: unimod
            POSTGRES_USER: unimod
            POSTGRES_DB: unimod
        volumes:
            - ./pgdata:/var/lib/postgresql/data
        network_mode: host

I initially encountered this error:

postgres_1  | 2021-05-27 20:43:17.685 UTC [83] ERROR:  there is no unique constraint matching given keys for referenced table "Brick"
postgres_1  | 2021-05-27 20:43:17.685 UTC [83] STATEMENT:  
postgres_1  |   CREATE TABLE "ModificationToBrick" (
postgres_1  |           id SERIAL NOT NULL, 
postgres_1  |           brick_string VARCHAR(64), 
postgres_1  |           modification_id INTEGER, 
postgres_1  |           count INTEGER, 
postgres_1  |           PRIMARY KEY (id), 
postgres_1  |           FOREIGN KEY(brick_string) REFERENCES "Brick" (brick), 
postgres_1  |           FOREIGN KEY(modification_id) REFERENCES "Modification" (id)
postgres_1  |   )

I sort of blindly tried to fix this by adding a unique constraint on Brick.brick: https://github.com/radusuciu/pyteomics/commit/364413d361177ff7747ab858b8cdc63b399db6a3#diff-1ade65743552f19d20d8bcc9845a4166aefd0fe563acc01c5716402ff7cbaee7L303-R303

Similar errors then crop up on the Specificity and Element tables: https://github.com/radusuciu/pyteomics/commit/364413d361177ff7747ab858b8cdc63b399db6a3

After adding unique constraints for those other tables, I hit a different error.

postgres_1  | 2021-05-27 21:34:23.830 UTC [189] ERROR:  insert or update on table "ModificationToBrick" violates foreign key constraint "ModificationToBrick_brick_string_fkey"
postgres_1  | 2021-05-27 21:34:23.830 UTC [189] DETAIL:  Key (brick_string)=(O) is not present in table "Brick".
postgres_1  | 2021-05-27 21:34:23.830 UTC [189] STATEMENT:  INSERT INTO "ModificationToBrick" (id, brick_string, modification_id, count) VALUES (20034, 'O', 1, 1),(20033, 'C', 1, 2),(20032, 'H', 1, 2),(11872, 'O', 2,  -1),(11871, 'N', 2, 1),(11870, 'H', 2, 1),(19969, 'S', 3, 1),(19968, 'O', 3, 2),(19967, 'N', 3, 2),(19966, 'C', 3, 10),(19965, 'H', 3, 14),(19964, 'O', 4, 1),(19963, 'N', 4, 1),(19962, 'C', 4, 2),(19961, 'H', 4, 3),(14253, 'O', 5, 1),(14252, 'N', 5, 1),(14251, 'C', 5, 1),(14250, 'H', 5, 1),(18668, 'O', 6, 2),(18667, 'C', 6, 2),(18666, 'H', 6, 2),(20852, 'O', 7, 1),(20851, 'N', 7,  -1),(20850, 'H', 7,  -1),(7009, 'S', 8, 1),(7008, 'O', 8, 6),(7007, 'N', 8, 4),(7006, 'C', 8, 22),(7005, 'H', 8, 38),(7020, 'S', 9, 1),(7019, 'O', 9, 6),(7018, 'N', 9, 4),(7017, 'C', 9, 22),(7016, '2H', 9, 8),(7015, 'H', 9, 30),(5946, 'S', 10,  -1),(5945, 'O', 10, 1),(5944, 'C', 10,  -1),(5943, 'H', 10,  -2),(8388, 'S', 11,  -1),(8387, 'C', 11,  -1),(8386, 'H', 11,  -4),(6983, 'S', 12, 1),(6982, 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429, 1),(10927, 'O', 431, 1),(10926, 'C', 431, 16)

My best guess at this point was that maybe Brick did not exist. I wiped the slate clean (stop container, remove database folder, and then re-create). I hit another issue with some Crossreference URLs being longer than 128 chars, so I swapped to a TEXT type column from the original VARYING: https://github.com/radusuciu/pyteomics/commit/35ff6dc007f70b83d81772df1d03c2d6fd739b28

Then, I deleted all the postgres data and re-created the container once more, only to hit a new error:

postgres_1  | 2021-05-27 21:58:45.570 UTC [84] ERROR:  insert or update on table "Crossreference" violates foreign key constraint "Crossreference_source_id_fkey"
postgres_1  | 2021-05-27 21:58:45.570 UTC [84] DETAIL:  Key (source_id)=(2) is not present in table "CrossreferenceSource".
postgres_1  | 2021-05-27 21:58:45.570 UTC [84] STATEMENT:  INSERT INTO "Crossreference" (id, source_id, url, modification_id, text) VALUES (4843, 2, '', 53, '11327326'),(4844, 13, '', 53, 'Poli G, Schaur RJ., IUBMB Life 2000 Oct-Nov;50(4-5):315-21'),(2612, 13, '', 17, 'Krutzsch and Inman, Analytical Biochemistry, 209, 109-116, (1993)'),(2849, 2, '', 55, '3083866'),(4654, 2, '', 56, '11857757'),(4655, 2, '', 56, '11999733'),(4656, 2, '', 56, '12175151'),(4657, 13, '', 56, 'Controlling Deuterium isotope effects in comparative proteomics.     Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E..    Department of Chemistry,  Purdue University,  West Lafayette,  IN,  USA.    Analytical Chemistry  (2'),(3202, 7, '', 299, 'AA0114'),(3201, 16, '', 299, 'GGLU'),(3200, 7, '', 299, 'AA0363'),(4762, 13, '', 58, 'Comparative proteomics based on stable isotope labeling and affinity selection.     Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A.    Department of Chemistry,  Pu'),(2461, 13, '', 59, 'Comparative proteomics based on stable isotope labeling and affinity selection.     Regnier, Fred E.; Riggs, Larry; Zhang, Roujian; Xiong, Li; Liu, Peiran; Chakraborty, Asish; Seeley, Erin; Sioma, Cathy; Thompson, Robert A.    Department of Chemistry,  Pu'),(2616, 13, '', 64, 'Controlling Deuterium isotope effects in comparative proteomics.     Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E..    Department of Chemistry,  Purdue University,  West Lafayette,  IN,  USA.    Analytical Chemistry  (2'),(2627, 13, '', 65, 'Controlling Deuterium isotope effects in comparative proteomics.     Zhang, Roujian; Sioma, Cathy S.; Thompson, Robert A.; Xiong, Li; Regnier, Fred E..    Department of Chemistry,  Purdue University,  West Lafayette,  IN,  USA.    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Chem., 75(21):5817-24 (2003)'),(2406, 15, '', 327, '2005 ASMS poster Presentation TP 527'),(5502, 13, '', 329, 'Identifying and quantifying in vivo methylation sites by heavy methyl SILAC, Shao-En Ong et al., Nature methods 1(2) 2004, 1-8'),(2725, 14, 'http://www2.waters.com/watprod.nsf/newdocs/930494', 194, 'Waters Application Note 930494'),(2607, 2, '', 185, '12716131'),(3637, 13, '', 188, 'Ong, S-E, I. Kratchmarova, and M. Mann (2003). J Proteome Research 2: 173-181'),(4069, 14, 'http://etd.caltech.edu/etd/available/etd-09132005-120123/unrestricted/Chapter2.pdf', 895, 'Page 12 Scheme 1: (1) Structure of azidohomoalanine (2) Biotin-PEO-alkyne in our case PEO n=3 as in this publication'),(1673, 2, '', 368, '11212008'),(1676, 2, '', 360, '9252331'),(3307, 14, '', 353, 'http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB'),(1773, 7, '', 352, 'AA0121'),(1774, 16, '', 352, 'ALLYS'),(4343, 7, '', 2, 'AA0088'),(6138, 7, '', 1, 'AA0048'),(3317, 13, '', 350, 'Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.'),(2782, 13, '', 261, 'Wang et al. 2004. Rapid Commun Mass Spectrom. 18(1):96-102'),(2468, 2, '', 94, '11746907'),(2478, 13, 'http://dx.doi.org/10.1002/rcm.517', 95, 'Rapid Communications in Mass Spectrometry, Volume 15, Issue 24 , Pages 2387 - 2392'),(5919, 14, 'https://www.thermofisher.com/us/en/home/references/molecular-probes-the-handbook/crosslinking-and-photoactivatable-reagents/chemical-crosslinking-reagents.html#head2', 323, 'The Molecular Probes Handbook'),(3259, 14, 'http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB', 289, 'Introduction to Protein Labeling'),(2681, 13, '', 293, 'Peirce MJ, Wait R, Begum S, Saklatvala J, Cope AP (2004) Mol Cell Proteomics 3: 56-65'),(3313, 14, '', 357, 'http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB'),(2984, 13, '', 476, 'J. Mass Spectrom. 2005; 40: 238-249'),(2446, 13, '', 319, 'Uchida K, Sakai K, Itakura K, Osawa T, Toyokuni S. 1977. Protein modification by lipid peroxidation products: formation of malondialdehyde-derived N(epsilon)-(2-propenol)lysine in proteins. Arch Biochem Biophys. 346(1):45-52'),(2694, 15, '', 285, 'ASMS 2005: Panchaud et al. (Poster ThP 509) ''''Combining protein identification and quantitation: C-terminal isotope-coded tagging'''''),(4594, 2, '', 335, '11910026'),(1920, 13, '', 337, 'Rapid Commun. Mass Spectrom. 2002; 16: 999-1001'),(3283, 7, '', 122, 'AA0211'),(3282, 2, '', 122, '15799070'),(1675, 13, '', 360, 'Berlett, Barbara S.; Stadtman, Earl R. Journal of Biological Chemistry (1997), 272(33), 20313-20316.'),(3312, 14, '', 361, 'http://www.piercenet.com/Proteomics/browse.cfm?fldID=84EBE112-F871-4CA5-807F-47327153CFCB'),(3209, 12, '', 11, 'Donald Voet, Judith G. Voet (1995): Biochemistry; p 115'),(3892, 7, '', 27, 'AA0031'),(1772, 2, '', 352, '9252331'),(1771, 2, '', 352, '11120890'),(6809, 2, '', 7, '6838602'),(6808, 7, '', 7, 'AA0214'),(5090, 13, '', 170, 'Anal. 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postgres_1  |   Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition.
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Wipe the slate clean once more, and a new error that I think also hints at a table creation order issue:

postgres_1  | 2021-05-27 22:07:22.971 UTC [83] ERROR:  insert or update on table "Fragment" violates foreign key constraint "Fragment_modification_id_fkey"
postgres_1  | 2021-05-27 22:07:22.971 UTC [83] DETAIL:  Key (modification_id)=(12) is not present in table "Modification".
postgres_1  | 2021-05-27 22:07:22.971 UTC [83] STATEMENT:  INSERT INTO "Fragment" (id, modification_id) VALUES (1, 12),(2, 12),(3, 12),(4, 12),(5, 12),(6, 12),(7, 13),(8, 13),(9, 13),(10, 13),(11, 13),(12, 13)

I will continue to investigate a bit, but wanted to report this issue to see if you have any thoughts on whether or not I've identified a real bug, or made a mistake somewhere along the way. I am able to successfully load into a SQLite database, without any of the modifications that are present on my fork, so I might just import those tables into Postgres, or maybe query the SQLite database directly.

Thanks!

mobiusklein commented 3 years ago

Yes, those column constraints were based upon approximations, but SQLite doesn't really care about data types or sizes, and it's not strict about foreign keys. They're merely hints about what the user expects. I haven't experimented with loading it into any other RBMS, but it's fixable. I can investigate the dependency graph and adapt the type modifications from you if that's okay.

What's your use-case for loading this all into Postgres?

radusuciu commented 3 years ago

I'm already using Postgres for other data and would prefer to keep everything under one umbrella to enable joins from the Unimod table to others, but this isn't a strict requirement by any means as it's pretty easy to go from SQLite to Postgres or to accomplish what I want in application code.

I guess if you're not interested in supporting Postgres, maybe you could indicate so in the docs?