Mirror 32dcc87 from github.com/open-reaction-database/ord-data

README.md

@@ -1,12 +1,48 @@
----
-license: cc-by-sa-4.0
----
 # ord-data
 
+![](https://github.com/Open-Reaction-Database/ord-data/workflows/Validation/badge.svg)
+![](https://raw.githubusercontent.com/Open-Reaction-Database/ord-data/main/badges/reactions.svg)
+[![DOI](https://zenodo.org/badge/283813042.svg)](https://zenodo.org/badge/latestdoi/283813042)
+
+## Getting the Data
+
+**We recommend downloading the dataset from
+[Hugging Face](https://huggingface.co/datasets/open-reaction-database/ord-data)
+instead of cloning this repository with Git LFS.** GitHub LFS bandwidth is a
+shared, limited resource, and heavy cloning traffic can exhaust our monthly
+quota and block downloads for everyone. The Hugging Face mirror has no such
+limit.
+
+### Option 1 (recommended): Download from Hugging Face
+
+```bash
+pip install -r scripts/requirements.txt
+python scripts/download_from_huggingface.py
+```
+
+The script mirrors the `data/` directory from the Hugging Face dataset into
+your local checkout. Pass `--allow-pattern 'data/4d/*.pb.gz'` (repeatable) to
+download only a subset, or `--output-dir <path>` to write somewhere other
+than the repository root. If you don't need the Git history, you can also
+clone this repo *without* LFS objects and then run the script:
+
+```bash
+GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/open-reaction-database/ord-data.git
+cd ord-data
+python scripts/download_from_huggingface.py
+```
+
+### Option 2: Clone with Git LFS
+
+If you have access to Git LFS bandwidth and need the `.pb.gz` files in place
+as part of a normal clone, install [Git LFS](https://git-lfs.github.com)
+before cloning. Please prefer Option 1 when possible so we don't exhaust the
+shared LFS quota.
+
 ## Data Manipulation
 
 The `ord-data` repository contains the Open Reaction Database (ORD) in Google's Protobuf binary
-format, which is stored in the `data` directory. Currently, all the data are stored in e.g.
+format, which is stored in the [`data`](data) directory. Currently, all the data are stored in e.g.
 *.pb.gz format (compressed Protobuf binary files) for the sake of efficiency. The user can convert
 the data into human readable text format, *.pb.txt.
 
@@ -58,4 +94,16 @@ print(f"We have converted the {input_fname} to JSON format shown as below, \n{rx
 
 ## Contributing
 
-Please see the [Submission Workflow](https://docs.open-reaction-database.org/en/latest/submissions.html) documentation. Make sure to review the [license](https://github.com/open-reaction-database/ord-data/blob/main/LICENSE) and [terms of use](https://github.com/open-reaction-database/ord-data/blob/main/CONTRIBUTING.md#terms-of-use).
+Please see the [Submission Workflow](https://docs.open-reaction-database.org/en/latest/submissions.html) documentation. Make sure to review the [license](https://github.com/open-reaction-database/ord-data/blob/main/LICENSE) and [terms of use](https://github.com/open-reaction-database/ord-data/blob/main/CONTRIBUTING.md#terms-of-use).
+
+## Maintainer notes
+
+### Skipping the `Update submission` step
+
+The submission workflow's `Update submission` step runs `process_dataset.py
+--update --cleanup` to assign reaction/dataset IDs and timestamps to newly
+submitted files and rewrite them to the canonical on-disk format. For
+maintainer PRs that touch dataset files but should *not* be re-processed
+this way — e.g., format conversions or mass migrations of already-finalized
+data — apply the `skip-update-submission` label to the PR. The validation
+side of the workflow still runs.

data/00/ord_dataset-00005539a1e04c809a9a78647bea649c.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bf1686ca6edac300a61acb5a5ee006ab5fd61007962ae19062b3d3c7879f84a9
+size 274285

data/03/ord_dataset-0316886541d9435489859c2ad7edc863.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:786b10eb7815c92e07800b7005fbdd046f15158c834b05596c6b02d3d6d2128e
+size 24703

data/0c/ord_dataset-0c75d67751634f0594b24b9f498b77c2.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:00fe35e881dc9a02feaa9186eaf69a221a44f1a281ea1b01f593953ecd65ede6
+size 29842

data/10/ord_dataset-10b940e7982c4622b1e1ac879394aba6.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:79923835d81b529c5d771cd7dc0ad6707348e6ceecbe4528205c47bb6de1d044
+size 43989

data/11/ord_dataset-1158e351757f315b93cbcbe7bc55f38e.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d0fa5e21c621d16714bae1b9157022b5a3ea02db909a2af8d7b5b976f7c950b5
+size 1112719074

data/17/ord_dataset-172039a759a440219a68af62d203b79b.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e32594d22839eaae4554642845e4e9dfc6abcf4bcecece6b26f4be64ce3bf39c
+size 21417

data/1d/ord_dataset-1d3a1a6fb70d46c084602d0688967afc.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9351ed4883b04c23505e6a1e8a3e216f90b7b79fd1ca72fd18f33c33a94e71b2
+size 11740

data/20/ord_dataset-2038a3c967db4a32a8fbce288437e929.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:52dd1e2d44ff052592a9f78bd5c9aac454ad90ab7a7f2f9795c4e742f89644d3
+size 17627

data/2b/ord_dataset-2be11f57f3304e678ea8469baf6dd1bc.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c7d17ab4af3551a4b2883c6e18c1f3a49b6c19d30d37fad762802aeeb275d948
+size 112943

data/2b/ord_dataset-2be30f5d8dcd471aa6ad410bdee05902.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6846bf47bd0d9652d1164f1dbc65cf730502e117131778499b8a10a98ef828b7
+size 17947

data/31/ord_dataset-31989f1b2b9d4885b1dd2d9982da4517.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:60f4f1bf9fd81166ce59e3ad8915310b0af5bca13956cab3b331748c1d3194dd
+size 17258

data/35/ord_dataset-35a5a513f1dd44a3a97c88da99f81a00.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:59f2cdd054631bde7354e21fc7080f0b80ebf2b5379f8ccd78b2df79d86b25d8
+size 19743

data/3b/ord_dataset-3b5db90e337942ea886b8f5bc5e3aa72.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fce2d70c28db7100b3ca5c3f298484daf4c4043c11a18da066db16ad2e36012c
+size 43118

data/3b/ord_dataset-3b8a2ef300e145468579027f206a3ac8.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f8438f4490541ecd38d92208decc48ff33424d52772cc42701b7eb886fc14b8a
+size 184557

data/46/ord_dataset-46ff9a32d9e04016b9380b1b1ef949c3.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:39440ea3e5442dddbb4daccbc48fb53940724085327c0e3b82909e1fd8cc661a
+size 395126

data/47/ord_dataset-47eaacc46c3a4487bbdf99adb1a15e41.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7e09c98aa540e15d44959f03028590278bf508650950778568fd264d3a7535c4
+size 8261981

data/48/ord_dataset-488402f6ec0d441ca2f7d6fabea7c220.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d1b658a9ed389f226baa003488c226fbd00dc35c44fc8e5029ef74b030928788
+size 10249187

data/4d/ord_dataset-4d431564f3ef4e9c91d8da5836f4eae6.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:be51ac3256a9f6793893bd59878f44f223f50ad530a1f71da0c408abf36ef70a
+size 17114

data/52/ord_dataset-52bd3b0ec72c443aab113bcea09bf3f4.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e3bf70610705d361b92b40c09ceaffff3d4f66002e958e5ea9c47bba9095297a
+size 10583

data/54/ord_dataset-5415f83da68e4797856ddd330dda5c61.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a186a7a7264e94fd958787a5a6a9d810e9c9c00608f1c6e136416098c39a2165
+size 25251

data/54/ord_dataset-5481550056a14935b76e031fb94b88be.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:48508c30931b04b4fe2e3bee55b84c83d10f57578c1ed5ccddbfb81875575702
+size 7666127

data/55/ord_dataset-5540e162c09f4c04905ddc8ba9c931c6.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7e44b014c9041d86e00bc4fb4b70b3c6b3b94c0e35634467ace02c330efcd1a4
+size 13289

data/55/ord_dataset-55de08a995554f558c25fc43eac62359.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9e4c3fefafe68d6cb43d5a39b8c441f440ce0c4626abbbe695c922089557b0f7
+size 11719

data/5c/ord_dataset-5c9a10329a8a48968d18879a48bb8ab2.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a2ea1363cb895b590ae765e918f98f90d243d6caba763ed74543ae62e503b0b0
+size 712770

data/5e/ord_dataset-5e8318f0dda04b398c14f4c3adfeb32c.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:94de6b8e87229d5db4fe8c17212afa2d3563478ca32aee934cc449559cab0bca
+size 8027

data/5e/ord_dataset-5eb7f2689f4a42eba63ad9e37e49a5cd.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2f478e163ab9f9ee2f001172fc9f0c33b0a65ec2dc787c12298f6e85bc86f7a6
+size 11134

data/67/ord_dataset-675eddcaa6674ce3ae61e79bbc1e1c08.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1ecc5469785e55997f244eb5f8d6dbc78029cbb233bd6a140b5f02d5d01860a1
+size 114800

data/68/ord_dataset-68cb8b4b2b384e3d85b5b1efae58b203.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:36cea7705307a5e359a176ed3862994e3edc60ae4363fc2f3c5862affff6bb21
+size 419710

data/6a/ord_dataset-6a0bfcdf53a64c07987822162ae591e2.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f970251d44ad75b68c8f6b8f3f28ff97f540fb7967d3bbc9b7338a7d7290ed3a
+size 16175

data/7a/ord_dataset-7acd6ad2bf4d4cff841cad008ab726d5.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b6dfe8e151a396c5332668c015bce764d23c667240e443495990205c66e4a1e5
+size 72692

data/7d/ord_dataset-7d8f5fd922d4497d91cb81489b052746.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3d657d1eda5703b58b627565894890269b50b18e987709e70fd7968d83e59101
+size 194483

data/89/ord_dataset-89b083710e2d441aa0040c361d63359f.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9a5cbdae282df3da7249e7525b7ecb739e4892061abe1f66e62c3fd69736ad72
+size 21940

data/8d/ord_dataset-8d1e28ec1f6b4ee8ad372e0b5ed7a62e.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e4f7505229e29321b5615f32ec2edcf45c9bc531bee2810d2a8985319b7ee127
+size 20904

data/99/ord_dataset-99c23cf435dc42f1af884053bc8b11c7.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e01a389cac3e6cce5746ef54dbe6b8d3040d764f987b1fc13790f5aeff5598fa
+size 210626

data/9b/ord_dataset-9b8aa9a7835143ef8ce3f70abfab7545.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:195765643b4aaad79d9ed82de6737a4855b9f2716e0bc0aa10cff950b7604d39
+size 126909

data/a1/ord_dataset-a12fa15d036d489c971b0b514caeae52.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ea52ef52e2ecf3eb33d74ca3ffac14ef539357551d252fbc706e95f60c94fca6
+size 39322

data/ac/ord_dataset-ac78456835404910b3a4c840248b6ac9.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ec3befdf2d98c2d122b1e5b8046dfb2bca6b035a1c506c9e1a2ddc4992276d88
+size 126387

data/b4/ord_dataset-b440f8c90b6343189093770060fc4098.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d289e2e9fbb77df61faadeb65cfadfbee0216b05a7d209b3ae3b3aca04a9993a
+size 111495

data/bc/ord_dataset-bc349c19b4384756a2aee8aa525b6c2a.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d4dbdaba59ac728696dea5bc0cafed5c5ab3236cc37da6e29b73e8a792f3b4a3
+size 17150

data/c5/ord_dataset-c5b00523487a4211a194160edf45e9ab.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:73c04ce2acaf6cf2b6b3ecda8c623d2a321435f1f5830aedb0a0f1afd562bdc4
+size 179304

data/cb/ord_dataset-cbcc4048add7468e850b6ec42549c70d.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fd62fb8331a5d2d68337882bd711d04f085b6beec7ef1283945f7f72a8cefb81
+size 30311

data/ce/ord_dataset-ce5045aceb214cfc8bfd0ef3031e2737.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fba1e4a5d3f30708bb925e0d0b93d420c26b17707f45fceb34e579f5f624c772
+size 10361

data/d2/ord_dataset-d26118acda314269becc35db5c22dc59.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0a600968a24eff0a440e30685b2cb7b62030693605574105eb57b7f07329700b
+size 130893

data/d3/ord_dataset-d319c2a22ecf4ce59db1a18ae71d529c.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a8a81d79136a36e14614f2cf4469f13393d675d6393f07d96f19e569623ac887
+size 30174

data/d9/ord_dataset-d92976309c3a48a3a64a4cf5e7048086.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:78c17145099d29458960ffcb6cec7a8987efeae06b100004be2255ff28e54994
+size 3784674

data/e7/ord_dataset-e7830cd6b11158b43994ccfb5ee9acb3.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:428d777066426504896fc2a0352838caba173518056ce83b387d9701f67af08e
+size 104636029

data/ee/ord_dataset-eeba974d3c284aed86d1c1d442260a1e.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:dbf6dae9521463c542fa8abccd2a078742c8052c0af11db842d200d94403fac6
+size 36161

data/fc/ord_dataset-fc83743b978f4deea7d6856deacbfe53.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:14095b49acb35adf50d1ff065d7b9d2ccf01d37f57ccaebbb6ce8eddfd11f484
+size 12354

data/fe/ord_dataset-feaf1b793c6d408aaec1cac7cc3ceadc.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ebefbe9aba687f182d4f068e94be0f7fd71d1189bdb2eff2aca6fedf4d522bf3
+size 37643