go-db

内容来源：README.md（说明文档） · 原始地址 · 查看安装指南

原始内容

# go-db

go-db is a Python package that provides a convenient way to load Gene Ontology (GO) annotations from GAF files into a DuckDB database for efficient querying and analysis. It includes scripts for loading data, validating the loaded data against GO rules, and running common queries.


## Usage

Currently you must have the repo checked out and be in the root directory.

```
uv sync
uv run go-db --help
```

To see all options:

```
uv run go-db --help
```

You must also place a copy of `go.db` in the `db` directory.

## Loading from GAF

Given `data/mgi.gaf` as input:

```
uv run go-db load -d db/mgi.db data/mgi.gaf
```

Note that the (very smart) duckdb auto-CSV detector seems to do the right thing with GAFs
but this should be fully validated.

__NOTE__: gaf2 and 17 columns is assumed

The loader is very simple - it just wraps [src/go_db/gaf.ddl.sql](https://github.com/cmungall/go-db/blob/HEAD/src/go_db/gaf.ddl.sql)

This has two tables:

1. A "flat" table that is a denormalized representation (no parsing)
2. The normalized table where `|` separators are split into duckdb lists

The loader is basically a wrapper like a Makefile

## Validation

This is done automatically after loading, unless `--no-validate` is passed

It can also be run at any time with:

```
uv run go-db validate -d mgi.db
```

This is just a simple wrapper for the SQL views here:

[src/go_db/go_rules.sql](https://github.com/cmungall/go-db/blob/HEAD/src/go_db/go_rules.sql)

Only a handful are defined. These have not been checked
(I made them by giving claude the schema and a PDF of the go rules documentation)

## Closure queries

Attach a semsql build of GO (currently sqlite)

```
attach 'db/go.semsql.db';
```



## Benchmarking

This is currently incomplete but to give a sense, to load a 6G (compressed) GAF:

```
time uv run go-db -load -d gcrp.db goa_uniprot_gcrp.gaf.gz
2197.27s user 110.23s system 664% cpu 5:47.33 total
```

This is half a billion associations:

```
D select count(*) from gaf_association;
┌──────────────┐
│ count_star() │
│    int64     │
├──────────────┤
│    419521545 │
└──────────────┘
```

24k species:

```
D select count(DISTINCT db_object_taxon) from gaf_association;
┌─────────────────────────────────┐
│ count(DISTINCT db_object_taxon) │
│              int64              │
├─────────────────────────────────┤
│                           24196 │
└─────────────────────────────────┘
```

Note also that queries are fast, including closure queries; e.g annotations to descendants of nucleus:

```
D select count(*) from gaf_association as a, go.entailed_edge as e where ontology_class_ref=e.subject and e.object='GO:0005634';
┌──────────────┐
│ count_star() │
│    int64     │
├──────────────┤
│     41502387 │
└──────────────┘
```

Grouping queries are also fast

```
D select db_object_taxon, count(*) as n from gaf_association where evidence_type != 'IEA' group by all having n > 1000;
┌─────────────────┬────────┐
│ db_object_taxon │   n    │
│     varchar     │ int64  │
├─────────────────┼────────┤
│ taxon:284593    │   4682 │
│ taxon:2711      │  26982 │
│ taxon:3983      │  37494 │
│ taxon:29655     │  25902 │
│ taxon:3641      │  30616 │
│ taxon:6238      │  28824 │
│ taxon:10116     │ 339989 │
│ taxon:515635    │   1857 │
│ taxon:105231    │  15644 │
│ taxon:9031      │  28416 │
│ taxon:330879    │  27064 │
│ taxon:5786      │  16380 │
│ taxon:227321    │  28418 │
│ taxon:10228     │  21717 │
│ taxon:418459    │  15857 │
│ taxon:6239      │  58538 │
│ taxon:64091     │   1635 │
│ taxon:1392      │   4523 │
│ taxon:243274    │   2104 │
│ taxon:9646      │   1169 │
│     ·           │     ·  │
│     ·           │     ·  │
│     ·           │     ·  │
│ taxon:9913      │  93347 │
│ taxon:665079    │  15615 │
│ taxon:4097      │  71322 │
│ taxon:5888      │  45377 │
│ taxon:4558      │  36859 │
│ taxon:81824     │  15543 │
│ taxon:412133    │  28519 │
│ taxon:9823      │  50408 │
│ taxon:3702      │ 105487 │
│ taxon:4432      │  31943 │
│ taxon:9258      │  49353 │
│ taxon:3880      │  42008 │
│ taxon:15368     │  34756 │
│ taxon:294381    │  11247 │
│ taxon:10036     │   1262 │
│ taxon:188937    │   2578 │
│ taxon:436308    │   1340 │
│ taxon:184922    │   5977 │
│ taxon:289376    │   1992 │
│ taxon:10141     │   1818 │
├─────────────────┴────────┤
│   160 rows (40 shown)    │
└──────────────────────────┘
```

This takes a few seconds:

```
select * from GORULE_0000005_violations limit 100;
100% ▕████████████████████████████████████████████████████████████▏
┌───────────┬──────────┬───────────────────┬────────────┬────────────────────┬──────────────────────┬───┬──────────────────┬──────────────────────┬──────────────────────┬──────────────────────┬──────────────────────┐
│    db     │ local_id │ db_object_symbol  │ qualifiers │ ontology_class_ref │ supporting_referen…  │ … │     subject      │  with_or_from_list   │ supporting_referen…  │ db_object_synonyms…  │ annotation_extensi…  │
│  varchar  │ varchar  │      varchar      │  varchar   │      varchar       │       varchar        │   │     varchar      │      varchar[]       │      varchar[]       │      varchar[]       │      varchar[]       │
├───────────┼──────────┼───────────────────┼────────────┼────────────────────┼──────────────────────┼───┼──────────────────┼──────────────────────┼──────────────────────┼──────────────────────┼──────────────────────┤
│ UniProtKB │ E1BNK3   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:E1BNK3 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q5RCV3   │ NBN               │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q5RCV3 │ [UniProtKB:O60934]   │ [GO_REF:0000024]     │ [NBN]                │                      │
│ UniProtKB │ F7HFK5   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:F7HFK5 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB]               │                      │
│ UniProtKB │ Q6XV80   │ nbn.L             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q6XV80 │ [UniProtKB:O60934]   │ [GO_REF:0000024]     │ [nbn.L, NBS1, nbn,…  │                      │
│ UniProtKB │ G3TLB6   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:G3TLB6 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB]               │                      │
│ UniProtKB │ Q9Y366   │ IFT52             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q9Y366 │ [UniProtKB:Q946G4]   │ [GO_REF:0000024]     │ [IFT52, C20orf9, N…  │                      │
│ UniProtKB │ F7BZB1   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:F7BZB1 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB]               │                      │
│ UniProtKB │ G1L6S5   │ CRTAP             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:G1L6S5 │ [UniProtKB:Q90830]   │ [GO_REF:0000024]     │ [CRTAP]              │                      │
│ UniProtKB │ A6QLJ0   │ ERCC2             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:A6QLJ0 │ [UniProtKB:P18074]   │ [GO_REF:0000024]     │ [ERCC2]              │                      │
│ UniProtKB │ P02548   │ NEFL              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P02548 │ [UniProtKB:P07196]   │ [GO_REF:0000024]     │ [NEFL]               │                      │
│ UniProtKB │ Q5ZIK2   │ PDZD11            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q5ZIK2 │ [UniProtKB:Q5EBL8-1] │ [GO_REF:0000024]     │ [PDZD11, PDZK11, R…  │                      │
│ UniProtKB │ P97494   │ Gclc              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P97494 │ [UniProtKB:P48506]   │ [GO_REF:0000024]     │ [Gclc, Glclc]        │                      │
│ UniProtKB │ G1RTT5   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:G1RTT5 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q6DIA9   │ Fbxo27            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q6DIA9 │ [UniProtKB:Q8NI29]   │ [GO_REF:0000024]     │ [Fbxo27]             │                      │
│ UniProtKB │ Q1LZ75   │ ERCC1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q1LZ75 │ [UniProtKB:P07992]   │ [GO_REF:0000024]     │ [ERCC1]              │                      │
│ UniProtKB │ L5KRZ8   │ PAL_GLEAN10000575 │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:L5KRZ8 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [PAL_GLEAN10000575]  │                      │
│ UniProtKB │ Q811D0   │ Dlg1              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q811D0 │ [UniProtKB:Q12959]   │ [GO_REF:0000024]     │ [Dlg1, Dlgh1]        │                      │
│ UniProtKB │ Q28IT1   │ erlec1            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q28IT1 │ [UniProtKB:Q96DZ1]   │ [GO_REF:0000024]     │ [erlec1, TNeu121c1…  │                      │
│ UniProtKB │ Q60HG1   │ ERCC3             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q60HG1 │ [UniProtKB:P19447]   │ [GO_REF:0000024]     │ [ERCC3, QnpA-11695]  │                      │
│ UniProtKB │ Q2YDW7   │ Kmt5a             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q2YDW7 │ [UniProtKB:Q9NQR1]   │ [GO_REF:0000024]     │ [Kmt5a, Setd8]       │                      │
│     ·     │   ·      │   ·               │    ·       │     ·              │       ·              │ · │        ·         │         ·            │        ·             │       ·              │          ·           │
│     ·     │   ·      │   ·               │    ·       │     ·              │       ·              │ · │        ·         │         ·            │        ·             │       ·              │          ·           │
│     ·     │   ·      │   ·               │    ·       │     ·              │       ·              │ · │        ·         │         ·            │        ·             │       ·              │          ·           │
│ UniProtKB │ Q9H2M9   │ RAB3GAP2          │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q9H2M9 │ [UniProtKB:Q5U1Z0]   │ [GO_REF:0000024]     │ [RAB3GAP2, KIAA0839] │                      │
│ UniProtKB │ Q62108   │ Dlg4              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q62108 │ [UniProtKB:P31016]   │ [GO_REF:0000024]     │ [Dlg4, Dlgh4, Psd95] │                      │
│ UniProtKB │ P11942   │ Cd3g              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P11942 │ [UniProtKB:P09693]   │ [GO_REF:0000024]     │ [Cd3g]               │                      │
│ UniProtKB │ P68399   │ CSNK2A1           │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P68399 │ [UniProtKB:P68400]   │ [GO_REF:0000024]     │ [CSNK2A1, CK2A1]     │                      │
│ UniProtKB │ M3W421   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:M3W421 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q3SX24   │ FBXO6             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q3SX24 │ [UniProtKB:Q9QZN4]   │ [GO_REF:0000024]     │ [FBXO6, FBS2, FBX6]  │                      │
│ UniProtKB │ P18341   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P18341 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q8K2C7   │ Os9               │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q8K2C7 │ [UniProtKB:Q13438]   │ [GO_REF:0000024]     │ [Os9]                │                      │
│ UniProtKB │ C0H5E1   │ PF3D7_1326800     │ enables    │ GO:0005515         │ PMID:19103232        │ … │ UniProtKB:C0H5E1 │                      │ [PMID:19103232]      │ [PF3D7_1326800]      │                      │
│ UniProtKB │ I3N2Y6   │ CRTAP             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:I3N2Y6 │ [UniProtKB:Q90830]   │ [GO_REF:0000024]     │ [CRTAP]              │                      │
│ UniProtKB │ Q6NXB2   │ pdzd11            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q6NXB2 │ [UniProtKB:Q5EBL8-1] │ [GO_REF:0000024]     │ [pdzd11, pdzk11, z…  │                      │
│ UniProtKB │ P50414   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P50414 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q62696   │ Dlg1              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q62696 │ [UniProtKB:Q12959]   │ [GO_REF:0000024]     │ [Dlg1, Dlgh1]        │                      │
│ UniProtKB │ Q17QJ6   │ BCL10             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q17QJ6 │ [UniProtKB:O95999]   │ [GO_REF:0000024]     │ [BCL10]              │                      │
│ UniProtKB │ Q17QJ6   │ BCL10             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q17QJ6 │ [UniProtKB:O95999]   │ [GO_REF:0000024]     │ [BCL10]              │ [part_of(GO:003166…  │
│ UniProtKB │ Q9N0C8   │ FBXO27            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q9N0C8 │ [UniProtKB:Q8NI29]   │ [GO_REF:0000024]     │ [FBXO27, QccE-12959] │                      │
│ UniProtKB │ Q9DE07   │ NBN               │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q9DE07 │ [UniProtKB:O60934]   │ [GO_REF:0000024]     │ [NBN, NBS1]          │                      │
│ UniProtKB │ Q2YDJ8   │ KMT5A             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q2YDJ8 │ [UniProtKB:Q9NQR1]   │ [GO_REF:0000024]     │ [KMT5A, SETD8]       │                      │
│ UniProtKB │ S9YCI6   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:S9YCI6 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB, CB1_0007150…  │                      │
│ UniProtKB │ D2GYR4   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:D2GYR4 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB, PANDA_002160] │                      │
├───────────┴──────────┴───────────────────┴────────────┴────────────────────┴──────────────────────┴───┴──────────────────┴──────────────────────┴──────────────────────┴──────────────────────┴──────────────────────┤
│ 100 rows (40 shown)                                                                                                                                                                            22 columns (11 shown) │
└──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘

```

# Acknowledgements

This [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [monarch-project-template](https://github.com/monarch-initiative/monarch-project-template) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).

go-db

go-db is a Python package that provides a convenient way to load Gene Ontology (GO) annotations from GAF files into a DuckDB database for efficient querying and analysis. It includes scripts for loading data, validating the loaded data against GO rules, and running common queries.

Usage

Currently you must have the repo checked out and be in the root directory.

uv sync
uv run go-db --help

To see all options:

uv run go-db --help

You must also place a copy of go.db in the db directory.

Loading from GAF

Given data/mgi.gaf as input:

uv run go-db load -d db/mgi.db data/mgi.gaf

Note that the (very smart) duckdb auto-CSV detector seems to do the right thing with GAFs but this should be fully validated.

NOTE: gaf2 and 17 columns is assumed

The loader is very simple - it just wraps src/go_db/gaf.ddl.sql

This has two tables:

A "flat" table that is a denormalized representation (no parsing)
The normalized table where | separators are split into duckdb lists

The loader is basically a wrapper like a Makefile

Validation

This is done automatically after loading, unless --no-validate is passed

It can also be run at any time with:

uv run go-db validate -d mgi.db

This is just a simple wrapper for the SQL views here:

src/go_db/go_rules.sql

Only a handful are defined. These have not been checked (I made them by giving claude the schema and a PDF of the go rules documentation)

Closure queries

Attach a semsql build of GO (currently sqlite)

attach 'db/go.semsql.db';

Benchmarking

This is currently incomplete but to give a sense, to load a 6G (compressed) GAF:

time uv run go-db -load -d gcrp.db goa_uniprot_gcrp.gaf.gz
2197.27s user 110.23s system 664% cpu 5:47.33 total

This is half a billion associations:

D select count(*) from gaf_association;
┌──────────────┐
│ count_star() │
│    int64     │
├──────────────┤
│    419521545 │
└──────────────┘

24k species:

D select count(DISTINCT db_object_taxon) from gaf_association;
┌─────────────────────────────────┐
│ count(DISTINCT db_object_taxon) │
│              int64              │
├─────────────────────────────────┤
│                           24196 │
└─────────────────────────────────┘

Note also that queries are fast, including closure queries; e.g annotations to descendants of nucleus:

D select count(*) from gaf_association as a, go.entailed_edge as e where ontology_class_ref=e.subject and e.object='GO:0005634';
┌──────────────┐
│ count_star() │
│    int64     │
├──────────────┤
│     41502387 │
└──────────────┘

Grouping queries are also fast

D select db_object_taxon, count(*) as n from gaf_association where evidence_type != 'IEA' group by all having n > 1000;
┌─────────────────┬────────┐
│ db_object_taxon │   n    │
│     varchar     │ int64  │
├─────────────────┼────────┤
│ taxon:284593    │   4682 │
│ taxon:2711      │  26982 │
│ taxon:3983      │  37494 │
│ taxon:29655     │  25902 │
│ taxon:3641      │  30616 │
│ taxon:6238      │  28824 │
│ taxon:10116     │ 339989 │
│ taxon:515635    │   1857 │
│ taxon:105231    │  15644 │
│ taxon:9031      │  28416 │
│ taxon:330879    │  27064 │
│ taxon:5786      │  16380 │
│ taxon:227321    │  28418 │
│ taxon:10228     │  21717 │
│ taxon:418459    │  15857 │
│ taxon:6239      │  58538 │
│ taxon:64091     │   1635 │
│ taxon:1392      │   4523 │
│ taxon:243274    │   2104 │
│ taxon:9646      │   1169 │
│     ·           │     ·  │
│     ·           │     ·  │
│     ·           │     ·  │
│ taxon:9913      │  93347 │
│ taxon:665079    │  15615 │
│ taxon:4097      │  71322 │
│ taxon:5888      │  45377 │
│ taxon:4558      │  36859 │
│ taxon:81824     │  15543 │
│ taxon:412133    │  28519 │
│ taxon:9823      │  50408 │
│ taxon:3702      │ 105487 │
│ taxon:4432      │  31943 │
│ taxon:9258      │  49353 │
│ taxon:3880      │  42008 │
│ taxon:15368     │  34756 │
│ taxon:294381    │  11247 │
│ taxon:10036     │   1262 │
│ taxon:188937    │   2578 │
│ taxon:436308    │   1340 │
│ taxon:184922    │   5977 │
│ taxon:289376    │   1992 │
│ taxon:10141     │   1818 │
├─────────────────┴────────┤
│   160 rows (40 shown)    │
└──────────────────────────┘

This takes a few seconds:

select * from GORULE_0000005_violations limit 100;
100% ▕████████████████████████████████████████████████████████████▏
┌───────────┬──────────┬───────────────────┬────────────┬────────────────────┬──────────────────────┬───┬──────────────────┬──────────────────────┬──────────────────────┬──────────────────────┬──────────────────────┐
│    db     │ local_id │ db_object_symbol  │ qualifiers │ ontology_class_ref │ supporting_referen…  │ … │     subject      │  with_or_from_list   │ supporting_referen…  │ db_object_synonyms…  │ annotation_extensi…  │
│  varchar  │ varchar  │      varchar      │  varchar   │      varchar       │       varchar        │   │     varchar      │      varchar[]       │      varchar[]       │      varchar[]       │      varchar[]       │
├───────────┼──────────┼───────────────────┼────────────┼────────────────────┼──────────────────────┼───┼──────────────────┼──────────────────────┼──────────────────────┼──────────────────────┼──────────────────────┤
│ UniProtKB │ E1BNK3   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:E1BNK3 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q5RCV3   │ NBN               │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q5RCV3 │ [UniProtKB:O60934]   │ [GO_REF:0000024]     │ [NBN]                │                      │
│ UniProtKB │ F7HFK5   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:F7HFK5 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB]               │                      │
│ UniProtKB │ Q6XV80   │ nbn.L             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q6XV80 │ [UniProtKB:O60934]   │ [GO_REF:0000024]     │ [nbn.L, NBS1, nbn,…  │                      │
│ UniProtKB │ G3TLB6   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:G3TLB6 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB]               │                      │
│ UniProtKB │ Q9Y366   │ IFT52             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q9Y366 │ [UniProtKB:Q946G4]   │ [GO_REF:0000024]     │ [IFT52, C20orf9, N…  │                      │
│ UniProtKB │ F7BZB1   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:F7BZB1 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB]               │                      │
│ UniProtKB │ G1L6S5   │ CRTAP             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:G1L6S5 │ [UniProtKB:Q90830]   │ [GO_REF:0000024]     │ [CRTAP]              │                      │
│ UniProtKB │ A6QLJ0   │ ERCC2             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:A6QLJ0 │ [UniProtKB:P18074]   │ [GO_REF:0000024]     │ [ERCC2]              │                      │
│ UniProtKB │ P02548   │ NEFL              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P02548 │ [UniProtKB:P07196]   │ [GO_REF:0000024]     │ [NEFL]               │                      │
│ UniProtKB │ Q5ZIK2   │ PDZD11            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q5ZIK2 │ [UniProtKB:Q5EBL8-1] │ [GO_REF:0000024]     │ [PDZD11, PDZK11, R…  │                      │
│ UniProtKB │ P97494   │ Gclc              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P97494 │ [UniProtKB:P48506]   │ [GO_REF:0000024]     │ [Gclc, Glclc]        │                      │
│ UniProtKB │ G1RTT5   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:G1RTT5 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q6DIA9   │ Fbxo27            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q6DIA9 │ [UniProtKB:Q8NI29]   │ [GO_REF:0000024]     │ [Fbxo27]             │                      │
│ UniProtKB │ Q1LZ75   │ ERCC1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q1LZ75 │ [UniProtKB:P07992]   │ [GO_REF:0000024]     │ [ERCC1]              │                      │
│ UniProtKB │ L5KRZ8   │ PAL_GLEAN10000575 │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:L5KRZ8 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [PAL_GLEAN10000575]  │                      │
│ UniProtKB │ Q811D0   │ Dlg1              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q811D0 │ [UniProtKB:Q12959]   │ [GO_REF:0000024]     │ [Dlg1, Dlgh1]        │                      │
│ UniProtKB │ Q28IT1   │ erlec1            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q28IT1 │ [UniProtKB:Q96DZ1]   │ [GO_REF:0000024]     │ [erlec1, TNeu121c1…  │                      │
│ UniProtKB │ Q60HG1   │ ERCC3             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q60HG1 │ [UniProtKB:P19447]   │ [GO_REF:0000024]     │ [ERCC3, QnpA-11695]  │                      │
│ UniProtKB │ Q2YDW7   │ Kmt5a             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q2YDW7 │ [UniProtKB:Q9NQR1]   │ [GO_REF:0000024]     │ [Kmt5a, Setd8]       │                      │
│     ·     │   ·      │   ·               │    ·       │     ·              │       ·              │ · │        ·         │         ·            │        ·             │       ·              │          ·           │
│     ·     │   ·      │   ·               │    ·       │     ·              │       ·              │ · │        ·         │         ·            │        ·             │       ·              │          ·           │
│     ·     │   ·      │   ·               │    ·       │     ·              │       ·              │ · │        ·         │         ·            │        ·             │       ·              │          ·           │
│ UniProtKB │ Q9H2M9   │ RAB3GAP2          │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q9H2M9 │ [UniProtKB:Q5U1Z0]   │ [GO_REF:0000024]     │ [RAB3GAP2, KIAA0839] │                      │
│ UniProtKB │ Q62108   │ Dlg4              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q62108 │ [UniProtKB:P31016]   │ [GO_REF:0000024]     │ [Dlg4, Dlgh4, Psd95] │                      │
│ UniProtKB │ P11942   │ Cd3g              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P11942 │ [UniProtKB:P09693]   │ [GO_REF:0000024]     │ [Cd3g]               │                      │
│ UniProtKB │ P68399   │ CSNK2A1           │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P68399 │ [UniProtKB:P68400]   │ [GO_REF:0000024]     │ [CSNK2A1, CK2A1]     │                      │
│ UniProtKB │ M3W421   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:M3W421 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q3SX24   │ FBXO6             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q3SX24 │ [UniProtKB:Q9QZN4]   │ [GO_REF:0000024]     │ [FBXO6, FBS2, FBX6]  │                      │
│ UniProtKB │ P18341   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P18341 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q8K2C7   │ Os9               │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q8K2C7 │ [UniProtKB:Q13438]   │ [GO_REF:0000024]     │ [Os9]                │                      │
│ UniProtKB │ C0H5E1   │ PF3D7_1326800     │ enables    │ GO:0005515         │ PMID:19103232        │ … │ UniProtKB:C0H5E1 │                      │ [PMID:19103232]      │ [PF3D7_1326800]      │                      │
│ UniProtKB │ I3N2Y6   │ CRTAP             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:I3N2Y6 │ [UniProtKB:Q90830]   │ [GO_REF:0000024]     │ [CRTAP]              │                      │
│ UniProtKB │ Q6NXB2   │ pdzd11            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q6NXB2 │ [UniProtKB:Q5EBL8-1] │ [GO_REF:0000024]     │ [pdzd11, pdzk11, z…  │                      │
│ UniProtKB │ P50414   │ TGFB1             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:P50414 │ [UniProtKB:P01137]   │ [GO_REF:0000024]     │ [TGFB1]              │                      │
│ UniProtKB │ Q62696   │ Dlg1              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q62696 │ [UniProtKB:Q12959]   │ [GO_REF:0000024]     │ [Dlg1, Dlgh1]        │                      │
│ UniProtKB │ Q17QJ6   │ BCL10             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q17QJ6 │ [UniProtKB:O95999]   │ [GO_REF:0000024]     │ [BCL10]              │                      │
│ UniProtKB │ Q17QJ6   │ BCL10             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q17QJ6 │ [UniProtKB:O95999]   │ [GO_REF:0000024]     │ [BCL10]              │ [part_of(GO:003166…  │
│ UniProtKB │ Q9N0C8   │ FBXO27            │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q9N0C8 │ [UniProtKB:Q8NI29]   │ [GO_REF:0000024]     │ [FBXO27, QccE-12959] │                      │
│ UniProtKB │ Q9DE07   │ NBN               │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q9DE07 │ [UniProtKB:O60934]   │ [GO_REF:0000024]     │ [NBN, NBS1]          │                      │
│ UniProtKB │ Q2YDJ8   │ KMT5A             │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:Q2YDJ8 │ [UniProtKB:Q9NQR1]   │ [GO_REF:0000024]     │ [KMT5A, SETD8]       │                      │
│ UniProtKB │ S9YCI6   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:S9YCI6 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB, CB1_0007150…  │                      │
│ UniProtKB │ D2GYR4   │ PPIB              │ enables    │ GO:0005515         │ GO_REF:0000024       │ … │ UniProtKB:D2GYR4 │ [UniProtKB:P24367]   │ [GO_REF:0000024]     │ [PPIB, PANDA_002160] │                      │
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Acknowledgements

This cookiecutter project was developed from the monarch-project-template template and will be kept up-to-date using cruft.