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data/FB15k-237/test.txt
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data/FB15k-237/test.txt
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data/FB15k-237/train.txt
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data/FB15k-237/valid.txt
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data/FB15k-237/valid.txt
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data/WN18RR/test.txt
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data/WN18RR/test.txt
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data/WN18RR/train.txt
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data/WN18RR/train.txt
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data/WN18RR/valid.txt
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data/WN18RR/valid.txt
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@ -1,2 +0,0 @@
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from .data_module import KGC
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from .processor import convert_examples_to_features, KGProcessor
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@ -1,63 +0,0 @@
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# Copyright (c) Microsoft Corporation.
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# Licensed under the MIT License.
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import cython
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from cython.parallel cimport prange, parallel
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cimport numpy
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import numpy
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def floyd_warshall(adjacency_matrix):
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(nrows, ncols) = adjacency_matrix.shape
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assert nrows == ncols
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cdef unsigned int n = nrows
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adj_mat_copy = adjacency_matrix.astype(long, order='C', casting='safe', copy=True)
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assert adj_mat_copy.flags['C_CONTIGUOUS']
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cdef numpy.ndarray[long, ndim=2, mode='c'] M = adj_mat_copy
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cdef numpy.ndarray[long, ndim=2, mode='c'] path = numpy.zeros([n, n], dtype=numpy.int64)
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cdef unsigned int i, j, k
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cdef long M_ij, M_ik, cost_ikkj
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cdef long* M_ptr = &M[0,0]
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cdef long* M_i_ptr
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cdef long* M_k_ptr
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# set unreachable nodes distance to 510
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for i in range(n):
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for j in range(n):
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if i == j:
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M[i][j] = 0
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elif M[i][j] == 0:
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M[i][j] = 510
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# floyed algo
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for k in range(n):
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M_k_ptr = M_ptr + n*k
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for i in range(n):
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M_i_ptr = M_ptr + n*i
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M_ik = M_i_ptr[k]
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for j in range(n):
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cost_ikkj = M_ik + M_k_ptr[j]
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M_ij = M_i_ptr[j]
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if M_ij > cost_ikkj:
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M_i_ptr[j] = cost_ikkj
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path[i][j] = k
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# set unreachable path to 510
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for i in range(n):
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for j in range(n):
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if M[i][j] >= 510:
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path[i][j] = 510
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M[i][j] = 510
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return M, path
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def get_all_edges(path, i, j):
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cdef unsigned int k = path[i][j]
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if k == 0:
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return []
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else:
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return get_all_edges(path, i, k) + [k] + get_all_edges(path, k, j)
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@ -1,71 +0,0 @@
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"""Base DataModule class."""
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from pathlib import Path
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from typing import Dict
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import argparse
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import os
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import pytorch_lightning as pl
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from torch.utils.data import DataLoader
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class Config(dict):
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def __getattr__(self, name):
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return self.get(name)
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def __setattr__(self, name, val):
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self[name] = val
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BATCH_SIZE = 8
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NUM_WORKERS = 8
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class BaseDataModule(pl.LightningDataModule):
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"""
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Base DataModule.
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Learn more at https://pytorch-lightning.readthedocs.io/en/stable/datamodules.html
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"""
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def __init__(self, args: argparse.Namespace = None) -> None:
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super().__init__()
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self.args = Config(vars(args)) if args is not None else {}
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self.batch_size = self.args.get("batch_size", BATCH_SIZE)
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self.num_workers = self.args.get("num_workers", NUM_WORKERS)
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@staticmethod
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def add_to_argparse(parser):
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parser.add_argument(
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"--batch_size", type=int, default=BATCH_SIZE, help="Number of examples to operate on per forward step."
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)
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parser.add_argument(
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"--num_workers", type=int, default=0, help="Number of additional processes to load data."
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)
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parser.add_argument(
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"--dataset", type=str, default="./dataset/NELL", help="Number of additional processes to load data."
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)
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return parser
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def prepare_data(self):
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"""
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Use this method to do things that might write to disk or that need to be done only from a single GPU in distributed settings (so don't set state `self.x = y`).
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"""
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pass
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def setup(self, stage=None):
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"""
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Split into train, val, test, and set dims.
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Should assign `torch Dataset` objects to self.data_train, self.data_val, and optionally self.data_test.
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"""
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self.data_train = None
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self.data_val = None
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self.data_test = None
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def train_dataloader(self):
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return DataLoader(self.data_train, shuffle=True, batch_size=self.batch_size, num_workers=self.num_workers, pin_memory=True)
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def val_dataloader(self):
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return DataLoader(self.data_val, shuffle=False, batch_size=self.batch_size, num_workers=self.num_workers, pin_memory=True)
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def test_dataloader(self):
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return DataLoader(self.data_test, shuffle=False, batch_size=self.batch_size, num_workers=self.num_workers, pin_memory=True)
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@ -1,195 +0,0 @@
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from dataclasses import dataclass
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from typing import Any, Callable, Dict, List, NewType, Optional, Tuple, Union
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from enum import Enum
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import torch
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from torch.utils.data import DataLoader
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from transformers import AutoTokenizer, BertTokenizer
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# from transformers.configuration_bert import BertTokenizer, BertTokenizerFast
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from transformers.tokenization_utils_base import (BatchEncoding,
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PreTrainedTokenizerBase)
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from .base_data_module import BaseDataModule
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from .processor import KGProcessor, get_dataset
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import transformers
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transformers.logging.set_verbosity_error()
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class ExplicitEnum(Enum):
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"""
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Enum with more explicit error message for missing values.
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"""
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@classmethod
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def _missing_(cls, value):
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raise ValueError(
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f"{value} is not a valid {cls.__name__}, please select one of {list(cls._value2member_map_.keys())}"
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)
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class PaddingStrategy(ExplicitEnum):
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"""
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Possible values for the ``padding`` argument in :meth:`PreTrainedTokenizerBase.__call__`. Useful for tab-completion
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in an IDE.
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"""
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LONGEST = "longest"
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MAX_LENGTH = "max_length"
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DO_NOT_PAD = "do_not_pad"
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import numpy as np
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@dataclass
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class DataCollatorForSeq2Seq:
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"""
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Data collator that will dynamically pad the inputs received, as well as the labels.
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Args:
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tokenizer (:class:`~transformers.PreTrainedTokenizer` or :class:`~transformers.PreTrainedTokenizerFast`):
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The tokenizer used for encoding the data.
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model (:class:`~transformers.PreTrainedModel`):
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The model that is being trained. If set and has the `prepare_decoder_input_ids_from_labels`, use it to
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prepare the `decoder_input_ids`
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This is useful when using `label_smoothing` to avoid calculating loss twice.
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padding (:obj:`bool`, :obj:`str` or :class:`~transformers.file_utils.PaddingStrategy`, `optional`, defaults to :obj:`True`):
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Select a strategy to pad the returned sequences (according to the model's padding side and padding index)
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among:
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* :obj:`True` or :obj:`'longest'`: Pad to the longest sequence in the batch (or no padding if only a single
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sequence is provided).
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* :obj:`'max_length'`: Pad to a maximum length specified with the argument :obj:`max_length` or to the
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maximum acceptable input length for the model if that argument is not provided.
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* :obj:`False` or :obj:`'do_not_pad'` (default): No padding (i.e., can output a batch with sequences of
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different lengths).
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max_length (:obj:`int`, `optional`):
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Maximum length of the returned list and optionally padding length (see above).
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pad_to_multiple_of (:obj:`int`, `optional`):
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If set will pad the sequence to a multiple of the provided value.
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This is especially useful to enable the use of Tensor Cores on NVIDIA hardware with compute capability >=
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7.5 (Volta).
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label_pad_token_id (:obj:`int`, `optional`, defaults to -100):
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The id to use when padding the labels (-100 will be automatically ignored by PyTorch loss functions).
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"""
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tokenizer: PreTrainedTokenizerBase
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model: Optional[Any] = None
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padding: Union[bool, str, PaddingStrategy] = True
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max_length: Optional[int] = None
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pad_to_multiple_of: Optional[int] = None
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label_pad_token_id: int = -100
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return_tensors: str = "pt"
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num_labels: int = 0
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def __call__(self, features, return_tensors=None):
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if return_tensors is None:
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return_tensors = self.return_tensors
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labels = [feature.pop("labels") for feature in features] if "labels" in features[0].keys() else None
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label = [feature.pop("label") for feature in features]
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features_keys = {}
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name_keys = list(features[0].keys())
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for k in name_keys:
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# ignore the padding arguments
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if k in ["input_ids", "attention_mask", "token_type_ids"]: continue
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try:
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features_keys[k] = [feature.pop(k) for feature in features]
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except KeyError:
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continue
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# We have to pad the labels before calling `tokenizer.pad` as this method won't pad them and needs them of the
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# same length to return tensors.
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bsz = len(labels)
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with torch.no_grad():
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new_labels = torch.zeros(bsz, self.num_labels)
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for i,l in enumerate(labels):
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if isinstance(l, int):
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new_labels[i][l] = 1
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else:
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for j in l:
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new_labels[i][j] = 1
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labels = new_labels
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features = self.tokenizer.pad(
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features,
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padding=self.padding,
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max_length=self.max_length,
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pad_to_multiple_of=self.pad_to_multiple_of,
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return_tensors=return_tensors,
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)
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features['labels'] = labels
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features['label'] = torch.tensor(label)
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features.update(features_keys)
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return features
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class KGC(BaseDataModule):
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def __init__(self, args, model) -> None:
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super().__init__(args)
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self.tokenizer = AutoTokenizer.from_pretrained(self.args.model_name_or_path, use_fast=False)
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self.processor = KGProcessor(self.tokenizer, args)
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self.label_list = self.processor.get_labels(args.data_dir)
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entity_list = self.processor.get_entities(args.data_dir)
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num_added_tokens = self.tokenizer.add_special_tokens({'additional_special_tokens': entity_list})
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self.sampler = DataCollatorForSeq2Seq(self.tokenizer,
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model=model,
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label_pad_token_id=self.tokenizer.pad_token_id,
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pad_to_multiple_of=8 if self.args.precision == 16 else None,
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padding="longest",
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max_length=self.args.max_seq_length,
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num_labels = len(entity_list),
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)
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relations_tokens = self.processor.get_relations(args.data_dir)
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self.num_relations = len(relations_tokens)
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num_added_tokens = self.tokenizer.add_special_tokens({'additional_special_tokens': relations_tokens})
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vocab = self.tokenizer.get_added_vocab()
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self.relation_id_st = vocab[relations_tokens[0]]
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self.relation_id_ed = vocab[relations_tokens[-1]] + 1
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self.entity_id_st = vocab[entity_list[0]]
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self.entity_id_ed = vocab[entity_list[-1]] + 1
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def setup(self, stage=None):
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self.data_train = get_dataset(self.args, self.processor, self.label_list, self.tokenizer, "train")
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self.data_val = get_dataset(self.args, self.processor, self.label_list, self.tokenizer, "dev")
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self.data_test = get_dataset(self.args, self.processor, self.label_list, self.tokenizer, "test")
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def prepare_data(self):
|
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pass
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|
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def get_config(self):
|
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d = {}
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for k, v in self.__dict__.items():
|
||||
if "st" in k or "ed" in k:
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d.update({k:v})
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return d
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|
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|
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@staticmethod
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def add_to_argparse(parser):
|
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BaseDataModule.add_to_argparse(parser)
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parser.add_argument("--model_name_or_path", type=str, default="roberta-base", help="the name or the path to the pretrained model")
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parser.add_argument("--data_dir", type=str, default="roberta-base", help="the name or the path to the pretrained model")
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parser.add_argument("--max_seq_length", type=int, default=256, help="Number of examples to operate on per forward step.")
|
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parser.add_argument("--warm_up_radio", type=float, default=0.1, help="Number of examples to operate on per forward step.")
|
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parser.add_argument("--eval_batch_size", type=int, default=8)
|
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parser.add_argument("--overwrite_cache", action="store_true", default=False)
|
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return parser
|
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|
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def get_tokenizer(self):
|
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return self.tokenizer
|
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|
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def train_dataloader(self):
|
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return DataLoader(self.data_train, num_workers=self.num_workers, pin_memory=True, collate_fn=self.sampler, batch_size=self.args.batch_size, shuffle=not self.args.faiss_init)
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|
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def val_dataloader(self):
|
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return DataLoader(self.data_val, num_workers=self.num_workers, pin_memory=True, collate_fn=self.sampler, batch_size=self.args.eval_batch_size)
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|
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def test_dataloader(self):
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return DataLoader(self.data_test, num_workers=self.num_workers, pin_memory=True, collate_fn=self.sampler, batch_size=self.args.eval_batch_size)
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1074
data/kinship/test.txt
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data/kinship/test.txt
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data/kinship/train.txt
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data/kinship/train.txt
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data/kinship/valid.txt
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data/kinship/valid.txt
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@ -1,954 +0,0 @@
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from hashlib import new
|
||||
from re import DEBUG
|
||||
|
||||
import contextlib
|
||||
import sys
|
||||
|
||||
from collections import Counter
|
||||
from multiprocessing import Pool
|
||||
from torch._C import HOIST_CONV_PACKED_PARAMS
|
||||
from torch.utils.data import Dataset, Sampler, IterableDataset
|
||||
from collections import defaultdict
|
||||
from functools import partial
|
||||
from multiprocessing import Pool
|
||||
import os
|
||||
import random
|
||||
import json
|
||||
import torch
|
||||
import copy
|
||||
import numpy as np
|
||||
import pickle
|
||||
from tqdm import tqdm
|
||||
from dataclasses import dataclass, asdict, replace
|
||||
import inspect
|
||||
|
||||
from transformers.models.auto.tokenization_auto import AutoTokenizer
|
||||
|
||||
from models.utils import get_entity_spans_pre_processing
|
||||
import pyximport
|
||||
|
||||
pyximport.install(setup_args={'include_dirs': np.get_include()})
|
||||
import data.algos as algos
|
||||
|
||||
def lmap(a, b):
|
||||
return list(map(a,b)) # a是个函数，b是个值列表，返回函数值列表
|
||||
|
||||
def cache_results(_cache_fp, _refresh=False, _verbose=1):
|
||||
r"""
|
||||
cache_results是fastNLP中用于cache数据的装饰器。通过下面的例子看一下如何使用::
|
||||
|
||||
import time
|
||||
import numpy as np
|
||||
from fastNLP import cache_results
|
||||
|
||||
@cache_results('cache.pkl')
|
||||
def process_data():
|
||||
# 一些比较耗时的工作，比如读取数据，预处理数据等，这里用time.sleep()代替耗时
|
||||
time.sleep(1)
|
||||
return np.random.randint(10, size=(5,))
|
||||
|
||||
start_time = time.time()
|
||||
print("res =",process_data())
|
||||
print(time.time() - start_time)
|
||||
|
||||
start_time = time.time()
|
||||
print("res =",process_data())
|
||||
print(time.time() - start_time)
|
||||
|
||||
# 输出内容如下，可以看到两次结果相同，且第二次几乎没有花费时间
|
||||
# Save cache to cache.pkl.
|
||||
# res = [5 4 9 1 8]
|
||||
# 1.0042750835418701
|
||||
# Read cache from cache.pkl.
|
||||
# res = [5 4 9 1 8]
|
||||
# 0.0040721893310546875
|
||||
|
||||
可以看到第二次运行的时候，只用了0.0001s左右，是由于第二次运行将直接从cache.pkl这个文件读取数据，而不会经过再次预处理::
|
||||
|
||||
# 还是以上面的例子为例，如果需要重新生成另一个cache，比如另一个数据集的内容，通过如下的方式调用即可
|
||||
process_data(_cache_fp='cache2.pkl') # 完全不影响之前的‘cache.pkl'
|
||||
|
||||
上面的_cache_fp是cache_results会识别的参数，它将从'cache2.pkl'这里缓存/读取数据，即这里的'cache2.pkl'覆盖默认的
|
||||
'cache.pkl'。如果在你的函数前面加上了@cache_results()则你的函数会增加三个参数[_cache_fp, _refresh, _verbose]。
|
||||
上面的例子即为使用_cache_fp的情况，这三个参数不会传入到你的函数中，当然你写的函数参数名也不可能包含这三个名称::
|
||||
|
||||
process_data(_cache_fp='cache2.pkl', _refresh=True) # 这里强制重新生成一份对预处理的cache。
|
||||
# _verbose是用于控制输出信息的，如果为0,则不输出任何内容;如果为1,则会提醒当前步骤是读取的cache还是生成了新的cache
|
||||
|
||||
:param str _cache_fp: 将返回结果缓存到什么位置;或从什么位置读取缓存。如果为None，cache_results没有任何效用，除非在
|
||||
函数调用的时候传入_cache_fp这个参数。
|
||||
:param bool _refresh: 是否重新生成cache。
|
||||
:param int _verbose: 是否打印cache的信息。
|
||||
:return:
|
||||
"""
|
||||
|
||||
def wrapper_(func):
|
||||
signature = inspect.signature(func)
|
||||
for key, _ in signature.parameters.items():
|
||||
if key in ('_cache_fp', '_refresh', '_verbose'):
|
||||
raise RuntimeError("The function decorated by cache_results cannot have keyword `{}`.".format(key))
|
||||
|
||||
def wrapper(*args, **kwargs):
|
||||
my_args = args[0]
|
||||
mode = args[-1]
|
||||
if '_cache_fp' in kwargs:
|
||||
cache_filepath = kwargs.pop('_cache_fp')
|
||||
assert isinstance(cache_filepath, str), "_cache_fp can only be str."
|
||||
else:
|
||||
cache_filepath = _cache_fp
|
||||
if '_refresh' in kwargs:
|
||||
refresh = kwargs.pop('_refresh')
|
||||
assert isinstance(refresh, bool), "_refresh can only be bool."
|
||||
else:
|
||||
refresh = _refresh
|
||||
if '_verbose' in kwargs:
|
||||
verbose = kwargs.pop('_verbose')
|
||||
assert isinstance(verbose, int), "_verbose can only be integer."
|
||||
else:
|
||||
verbose = _verbose
|
||||
refresh_flag = True
|
||||
|
||||
model_name = my_args.model_name_or_path.split("/")[-1]
|
||||
is_pretrain = my_args.pretrain
|
||||
cache_filepath = os.path.join(my_args.data_dir, f"cached_{mode}_features{model_name}_pretrain{is_pretrain}_faiss{my_args.faiss_init}_seqlength{my_args.max_seq_length}_{my_args.litmodel_class}.pkl")
|
||||
refresh = my_args.overwrite_cache
|
||||
|
||||
if cache_filepath is not None and refresh is False:
|
||||
# load data
|
||||
if os.path.exists(cache_filepath):
|
||||
with open(cache_filepath, 'rb') as f:
|
||||
results = pickle.load(f)
|
||||
if verbose == 1:
|
||||
logger.info("Read cache from {}.".format(cache_filepath))
|
||||
refresh_flag = False
|
||||
|
||||
if refresh_flag:
|
||||
results = func(*args, **kwargs)
|
||||
if cache_filepath is not None:
|
||||
if results is None:
|
||||
raise RuntimeError("The return value is None. Delete the decorator.")
|
||||
with open(cache_filepath, 'wb') as f:
|
||||
pickle.dump(results, f)
|
||||
logger.info("Save cache to {}.".format(cache_filepath))
|
||||
|
||||
return results
|
||||
|
||||
return wrapper
|
||||
|
||||
return wrapper_
|
||||
|
||||
|
||||
import argparse
|
||||
import csv
|
||||
import logging
|
||||
import os
|
||||
import random
|
||||
import sys
|
||||
|
||||
import numpy as np
|
||||
import torch
|
||||
from torch.utils.data import (DataLoader, RandomSampler, SequentialSampler,
|
||||
TensorDataset)
|
||||
from torch.utils.data.distributed import DistributedSampler
|
||||
from tqdm import tqdm, trange
|
||||
|
||||
# from torch.nn import CrossEntropyLoss, MSELoss
|
||||
# from scipy.stats import pearsonr, spearmanr
|
||||
# from sklearn.metrics import matthews_corrcoef, f1_scoreclass
|
||||
|
||||
|
||||
|
||||
logger = logging.getLogger(__name__)
|
||||
|
||||
class InputExample(object):
|
||||
"""A single training/test example for simple sequence classification."""
|
||||
|
||||
def __init__(self, guid, text_a, text_b=None, text_c=None, text_d=None, label=None, real_label=None, en=None, en_id=None, rel=None, text_d_id=None, graph_inf=None):
|
||||
"""Constructs a InputExample.
|
||||
|
||||
Args:
|
||||
guid: Unique id for the example.
|
||||
text_a: string. The untokenized text of the first sequence. For single
|
||||
sequence tasks, only this sequence must be specified.
|
||||
text_b: (Optional) string. The untokenized text of the second sequence.
|
||||
Only must be specified for sequence pair tasks.
|
||||
text_c: (Optional) string. The untokenized text of the third sequence.
|
||||
Only must be specified for sequence triple tasks.
|
||||
label: (Optional) string. list of entities
|
||||
"""
|
||||
self.guid = guid
|
||||
self.text_a = text_a
|
||||
self.text_b = text_b
|
||||
self.text_c = text_c
|
||||
self.text_d = text_d
|
||||
self.label = label
|
||||
self.real_label = real_label
|
||||
self.en = en
|
||||
self.rel = rel # rel id
|
||||
self.text_d_id = text_d_id
|
||||
self.graph_inf = graph_inf
|
||||
self.en_id = en_id
|
||||
|
||||
|
||||
@dataclass
|
||||
class InputFeatures:
|
||||
"""A single set of features of data."""
|
||||
|
||||
input_ids: torch.Tensor
|
||||
attention_mask: torch.Tensor
|
||||
labels: torch.Tensor = None
|
||||
label: torch.Tensor = None
|
||||
en: torch.Tensor = 0
|
||||
rel: torch.Tensor = 0
|
||||
pos: torch.Tensor = 0
|
||||
graph: torch.Tensor = 0
|
||||
distance_attention: torch.Tensor = 0
|
||||
# attention_bias: torch.Tensor = 0
|
||||
|
||||
|
||||
class DataProcessor(object):
|
||||
"""Base class for data converters for sequence classification data sets."""
|
||||
|
||||
def get_train_examples(self, data_dir):
|
||||
"""Gets a collection of `InputExample`s for the train set."""
|
||||
raise NotImplementedError()
|
||||
|
||||
def get_dev_examples(self, data_dir):
|
||||
"""Gets a collection of `InputExample`s for the dev set."""
|
||||
raise NotImplementedError()
|
||||
|
||||
def get_labels(self, data_dir):
|
||||
"""Gets the list of labels for this data set."""
|
||||
raise NotImplementedError()
|
||||
|
||||
@classmethod
|
||||
def _read_tsv(cls, input_file, quotechar=None):
|
||||
"""Reads a tab separated value file."""
|
||||
with open(input_file, "r", encoding="utf-8") as f:
|
||||
reader = csv.reader(f, delimiter="\t", quotechar=quotechar)
|
||||
lines = []
|
||||
for line in reader:
|
||||
if sys.version_info[0] == 2:
|
||||
line = list(unicode(cell, 'utf-8') for cell in line)
|
||||
lines.append(line)
|
||||
return lines
|
||||
|
||||
import copy
|
||||
|
||||
|
||||
def solve_get_knowledge_store(line, set_type="train", pretrain=1):
|
||||
"""
|
||||
use the LM to get the entity embedding.
|
||||
Transductive: triples + text description
|
||||
Inductive: text description
|
||||
|
||||
"""
|
||||
examples = []
|
||||
|
||||
head_ent_text = ent2text[line[0]]
|
||||
tail_ent_text = ent2text[line[2]]
|
||||
relation_text = rel2text[line[1]]
|
||||
|
||||
i=0
|
||||
|
||||
a = tail_filter_entities["\t".join([line[0],line[1]])]
|
||||
b = head_filter_entities["\t".join([line[2],line[1]])]
|
||||
|
||||
guid = "%s-%s" % (set_type, i)
|
||||
text_a = head_ent_text
|
||||
text_b = relation_text
|
||||
text_c = tail_ent_text
|
||||
|
||||
# use the description of c to predict A
|
||||
examples.append(
|
||||
InputExample(guid=guid, text_a="[PAD]", text_b=text_b + "[PAD]", text_c = "[PAD]" + " " + text_c, label=lmap(lambda x: ent2id[x], b), real_label=ent2id[line[0]], en=[ent2id[line[0]], rel2id[line[1]], ent2id[line[2]]], rel=0)
|
||||
)
|
||||
examples.append(
|
||||
InputExample(guid=guid, text_a="[PAD]", text_b=text_b + "[PAD]", text_c = "[PAD]" + " " + text_a, label=lmap(lambda x: ent2id[x], b), real_label=ent2id[line[2]], en=[ent2id[line[0]], rel2id[line[1]], ent2id[line[2]]], rel=0)
|
||||
)
|
||||
return examples
|
||||
|
||||
|
||||
def solve(line, set_type="train", pretrain=1, max_triplet=32):
|
||||
examples = []
|
||||
|
||||
head_ent_text = ent2text[line[0]]
|
||||
tail_ent_text = ent2text[line[2]]
|
||||
relation_text = rel2text[line[1]]
|
||||
|
||||
i=0
|
||||
|
||||
a = tail_filter_entities["\t".join([line[0],line[1]])]
|
||||
b = head_filter_entities["\t".join([line[2],line[1]])]
|
||||
|
||||
guid = "%s-%s" % (set_type, i)
|
||||
text_a = head_ent_text
|
||||
text_b = relation_text
|
||||
text_c = tail_ent_text
|
||||
|
||||
|
||||
if pretrain:
|
||||
text_a_tokens = text_a.split()
|
||||
for i in range(10):
|
||||
st = random.randint(0, len(text_a_tokens))
|
||||
examples.append(
|
||||
InputExample(guid=guid, text_a="[MASK]", text_b=" ".join(text_a_tokens[st:min(st+64, len(text_a_tokens))]), text_c = "", label=ent2id[line[0]], real_label=ent2id[line[0]], en=0, rel=0)
|
||||
)
|
||||
examples.append(
|
||||
InputExample(guid=guid, text_a="[MASK]", text_b=text_a, text_c = "", label=ent2id[line[0]], real_label=ent2id[line[0]], en=0, rel=0)
|
||||
)
|
||||
# examples.append(
|
||||
# InputExample(guid=guid, text_a="[MASK]", text_b=text_c, text_c = "", label=ent2id[line[2]], real_label=ent2id[line[2]], en=0, rel=0)
|
||||
# )
|
||||
else:
|
||||
# 主要是对text_c进行包装，不再是原来的文本，而是对应子图的graph（变量graph_seq）。如果mask的是尾实体，那么就让text_c在后面加入graph_seq
|
||||
# masked_head_seq = []
|
||||
# masked_tail_seq = []
|
||||
# masked_tail_graph_list = masked_tail_neighbor["\t".join([line[0],line[1]])]
|
||||
# masked_head_graph_list = masked_head_neighbor["\t".join([line[2],line[1]])]
|
||||
# for item in masked_head_graph_list:
|
||||
# masked_head_seq.append(ent2id[item[0]])
|
||||
# masked_head_seq.append(rel2id[item[1]])
|
||||
# masked_head_seq.append(ent2id[item[2]])
|
||||
|
||||
# for item in masked_tail_graph_list:
|
||||
# masked_tail_seq.append(ent2id[item[0]])
|
||||
# masked_tail_seq.append(rel2id[item[1]])
|
||||
# masked_tail_seq.append(ent2id[item[2]])
|
||||
|
||||
masked_head_seq = set()
|
||||
masked_head_seq_id = set()
|
||||
masked_tail_seq = set()
|
||||
masked_tail_seq_id = set()
|
||||
|
||||
masked_tail_graph_list = masked_tail_neighbor["\t".join([line[0],line[1]])] if len(masked_tail_neighbor["\t".join([line[0],line[1]])]) < max_triplet else \
|
||||
random.sample(masked_tail_neighbor["\t".join([line[0],line[1]])], max_triplet)
|
||||
masked_head_graph_list = masked_head_neighbor["\t".join([line[2],line[1]])] if len(masked_head_neighbor["\t".join([line[2],line[1]])]) < max_triplet else \
|
||||
random.sample(masked_head_neighbor["\t".join([line[2],line[1]])], max_triplet)
|
||||
# masked_tail_graph_list = masked_tail_neighbor["\t".join([line[0],line[1]])][:16]
|
||||
# masked_head_graph_list = masked_head_neighbor["\t".join([line[2],line[1]])][:16]
|
||||
for item in masked_head_graph_list:
|
||||
masked_head_seq.add(item[0])
|
||||
masked_head_seq.add(item[1])
|
||||
masked_head_seq.add(item[2])
|
||||
masked_head_seq_id.add(ent2id[item[0]])
|
||||
masked_head_seq_id.add(rel2id[item[1]])
|
||||
masked_head_seq_id.add(ent2id[item[2]])
|
||||
|
||||
for item in masked_tail_graph_list:
|
||||
masked_tail_seq.add(item[0])
|
||||
masked_tail_seq.add(item[1])
|
||||
masked_tail_seq.add(item[2])
|
||||
masked_tail_seq_id.add(ent2id[item[0]])
|
||||
masked_tail_seq_id.add(rel2id[item[1]])
|
||||
masked_tail_seq_id.add(ent2id[item[2]])
|
||||
# print(masked_tail_seq)
|
||||
masked_head_seq = masked_head_seq.difference({line[0]})
|
||||
masked_head_seq = masked_head_seq.difference({line[2]})
|
||||
masked_head_seq = masked_head_seq.difference({line[1]})
|
||||
masked_head_seq_id = masked_head_seq_id.difference({ent2id[line[0]]})
|
||||
masked_head_seq_id = masked_head_seq_id.difference({rel2id[line[1]]})
|
||||
masked_head_seq_id = masked_head_seq_id.difference({ent2id[line[2]]})
|
||||
|
||||
masked_tail_seq = masked_tail_seq.difference({line[0]})
|
||||
masked_tail_seq = masked_tail_seq.difference({line[2]})
|
||||
masked_tail_seq = masked_tail_seq.difference({line[1]})
|
||||
masked_tail_seq_id = masked_tail_seq_id.difference({ent2id[line[0]]})
|
||||
masked_tail_seq_id = masked_tail_seq_id.difference({rel2id[line[1]]})
|
||||
masked_tail_seq_id = masked_tail_seq_id.difference({ent2id[line[2]]})
|
||||
# examples.append(
|
||||
# InputExample(guid=guid, text_a="[MASK]", text_b=' '.join(text_b.split(' ')[:16]) + " [PAD]", text_c = "[PAD]" + " " + ' '.join(text_c.split(' ')[:16]), text_d = masked_head_seq, label=lmap(lambda x: ent2id[x], b), real_label=ent2id[line[0]], en=[rel2id[line[1]], ent2id[line[2]]], rel=rel2id[line[1]]))
|
||||
# examples.append(
|
||||
# InputExample(guid=guid, text_a="[PAD] ", text_b=' '.join(text_b.split(' ')[:16]) + " [PAD]", text_c = "[MASK]" +" " + ' '.join(text_a.split(' ')[:16]), text_d = masked_tail_seq, label=lmap(lambda x: ent2id[x], a), real_label=ent2id[line[2]], en=[ent2id[line[0]], rel2id[line[1]]], rel=rel2id[line[1]]))
|
||||
examples.append(
|
||||
InputExample(guid=guid, text_a="[MASK]", text_b="[PAD]", text_c = "[PAD]", text_d = list(masked_head_seq), label=lmap(lambda x: ent2id[x], b), real_label=ent2id[line[0]], en=[line[1], line[2]], en_id = [rel2id[line[1]], ent2id[line[2]]], rel=rel2id[line[1]], text_d_id = list(masked_head_seq_id), graph_inf = masked_head_graph_list))
|
||||
examples.append(
|
||||
InputExample(guid=guid, text_a="[PAD]", text_b="[PAD]", text_c = "[MASK]", text_d = list(masked_tail_seq), label=lmap(lambda x: ent2id[x], a), real_label=ent2id[line[2]], en=[line[0], line[1]], en_id = [ent2id[line[0]], rel2id[line[1]]], rel=rel2id[line[1]], text_d_id = list(masked_tail_seq_id), graph_inf = masked_tail_graph_list))
|
||||
return examples
|
||||
|
||||
def filter_init(head, tail, t1,t2, ent2id_, ent2token_, rel2id_, masked_head_neighbor_, masked_tail_neighbor_, rel2token_):
|
||||
global head_filter_entities
|
||||
global tail_filter_entities
|
||||
global ent2text
|
||||
global rel2text
|
||||
global ent2id
|
||||
global ent2token
|
||||
global rel2id
|
||||
global masked_head_neighbor
|
||||
global masked_tail_neighbor
|
||||
global rel2token
|
||||
|
||||
head_filter_entities = head
|
||||
tail_filter_entities = tail
|
||||
ent2text =t1
|
||||
rel2text =t2
|
||||
ent2id = ent2id_
|
||||
ent2token = ent2token_
|
||||
rel2id = rel2id_
|
||||
masked_head_neighbor = masked_head_neighbor_
|
||||
masked_tail_neighbor = masked_tail_neighbor_
|
||||
rel2token = rel2token_
|
||||
|
||||
def delete_init(ent2text_):
|
||||
global ent2text
|
||||
ent2text = ent2text_
|
||||
|
||||
|
||||
class KGProcessor(DataProcessor):
|
||||
"""Processor for knowledge graph data set."""
|
||||
def __init__(self, tokenizer, args):
|
||||
self.labels = set()
|
||||
self.tokenizer = tokenizer
|
||||
self.args = args
|
||||
self.entity_path = os.path.join(args.data_dir, "entity2textlong.txt") if os.path.exists(os.path.join(args.data_dir, 'entity2textlong.txt')) \
|
||||
else os.path.join(args.data_dir, "entity2text.txt")
|
||||
|
||||
def get_train_examples(self, data_dir):
|
||||
"""See base class."""
|
||||
return self._create_examples(
|
||||
self._read_tsv(os.path.join(data_dir, "train.tsv")), "train", data_dir, self.args)
|
||||
|
||||
def get_dev_examples(self, data_dir):
|
||||
"""See base class."""
|
||||
return self._create_examples(
|
||||
self._read_tsv(os.path.join(data_dir, "dev.tsv")), "dev", data_dir, self.args)
|
||||
|
||||
def get_test_examples(self, data_dir, chunk=""):
|
||||
"""See base class."""
|
||||
return self._create_examples(
|
||||
self._read_tsv(os.path.join(data_dir, f"test{chunk}.tsv")), "test", data_dir, self.args)
|
||||
|
||||
def get_relations(self, data_dir):
|
||||
"""Gets all labels (relations) in the knowledge graph."""
|
||||
# return list(self.labels)
|
||||
with open(os.path.join(data_dir, "relations.txt"), 'r') as f:
|
||||
lines = f.readlines()
|
||||
relations = []
|
||||
for line in lines:
|
||||
relations.append(line.strip().split('\t')[0])
|
||||
rel2token = {ent : f"[RELATION_{i}]" for i, ent in enumerate(relations)}
|
||||
return list(rel2token.values())
|
||||
|
||||
def get_labels(self, data_dir):
|
||||
"""Gets all labels (0, 1) for triples in the knowledge graph."""
|
||||
relation = []
|
||||
with open(os.path.join(data_dir, "relation2text.txt"), 'r') as f:
|
||||
lines = f.readlines()
|
||||
entities = []
|
||||
for line in lines:
|
||||
relation.append(line.strip().split("\t")[-1])
|
||||
return relation
|
||||
|
||||
def get_entities(self, data_dir):
|
||||
"""Gets all entities in the knowledge graph."""
|
||||
with open(self.entity_path, 'r') as f:
|
||||
lines = f.readlines()
|
||||
entities = []
|
||||
for line in lines:
|
||||
entities.append(line.strip().split("\t")[0])
|
||||
|
||||
ent2token = {ent : f"[ENTITY_{i}]" for i, ent in enumerate(entities)}
|
||||
return list(ent2token.values())
|
||||
|
||||
def get_train_triples(self, data_dir):
|
||||
"""Gets training triples."""
|
||||
return self._read_tsv(os.path.join(data_dir, "train.tsv"))
|
||||
|
||||
def get_dev_triples(self, data_dir):
|
||||
"""Gets validation triples."""
|
||||
return self._read_tsv(os.path.join(data_dir, "dev.tsv"))
|
||||
|
||||
def get_test_triples(self, data_dir, chunk=""):
|
||||
"""Gets test triples."""
|
||||
return self._read_tsv(os.path.join(data_dir, f"test{chunk}.tsv"))
|
||||
|
||||
def _create_examples(self, lines, set_type, data_dir, args):
|
||||
"""Creates examples for the training and dev sets."""
|
||||
# entity to text
|
||||
ent2text = {}
|
||||
ent2text_with_type = {}
|
||||
with open(self.entity_path, 'r') as f:
|
||||
ent_lines = f.readlines()
|
||||
for line in ent_lines:
|
||||
temp = line.strip().split('\t')
|
||||
try:
|
||||
end = temp[1]#.find(',')
|
||||
if "wiki" in data_dir:
|
||||
assert "Q" in temp[0]
|
||||
ent2text[temp[0]] = temp[1].replace("\\n", " ").replace("\\", "") #[:end]
|
||||
except IndexError:
|
||||
# continue
|
||||
end = " "#.find(',')
|
||||
if "wiki" in data_dir:
|
||||
assert "Q" in temp[0]
|
||||
ent2text[temp[0]] = end #[:end]
|
||||
|
||||
entities = list(ent2text.keys())
|
||||
ent2token = {ent : f"[ENTITY_{i}]" for i, ent in enumerate(entities)}
|
||||
ent2id = {ent : i for i, ent in enumerate(entities)}
|
||||
|
||||
rel2text = {}
|
||||
with open(os.path.join(data_dir, "relation2text.txt"), 'r') as f:
|
||||
rel_lines = f.readlines()
|
||||
for line in rel_lines:
|
||||
temp = line.strip().split('\t')
|
||||
rel2text[temp[0]] = temp[1]
|
||||
|
||||
relation_names = {}
|
||||
with open(os.path.join(data_dir, "relations.txt"), "r") as file:
|
||||
for line in file.readlines():
|
||||
t = line.strip()
|
||||
relation_names[t] = rel2text[t]
|
||||
|
||||
tmp_lines = []
|
||||
not_in_text = 0
|
||||
for line in tqdm(lines, desc="delete entities without text name."):
|
||||
if (line[0] not in ent2text) or (line[2] not in ent2text) or (line[1] not in rel2text):
|
||||
not_in_text += 1
|
||||
continue
|
||||
tmp_lines.append(line)
|
||||
lines = tmp_lines
|
||||
print(f"total entity not in text : {not_in_text} ")
|
||||
|
||||
relations = list(rel2text.keys())
|
||||
rel2token = {rel : f"[RELATION_{i}]" for i, rel in enumerate(relations)}
|
||||
# rel id -> relation token id
|
||||
num_entities = len(self.get_entities(args.data_dir))
|
||||
rel2id = {w:i+num_entities for i,w in enumerate(relation_names.keys())}
|
||||
|
||||
|
||||
with open(os.path.join(data_dir, "masked_head_neighbor.txt"), 'r') as file:
|
||||
masked_head_neighbor = json.load(file)
|
||||
|
||||
with open(os.path.join(data_dir, "masked_tail_neighbor.txt"), 'r') as file:
|
||||
masked_tail_neighbor = json.load(file)
|
||||
|
||||
examples = []
|
||||
# head filter head entity
|
||||
head_filter_entities = defaultdict(list)
|
||||
tail_filter_entities = defaultdict(list)
|
||||
|
||||
dataset_list = ["train.tsv", "dev.tsv", "test.tsv"]
|
||||
# in training, only use the train triples
|
||||
if set_type == "train" and not args.pretrain: dataset_list = dataset_list[0:1]
|
||||
for m in dataset_list:
|
||||
with open(os.path.join(data_dir, m), 'r') as file:
|
||||
train_lines = file.readlines()
|
||||
for idx in range(len(train_lines)):
|
||||
train_lines[idx] = train_lines[idx].strip().split("\t")
|
||||
|
||||
for line in train_lines:
|
||||
tail_filter_entities["\t".join([line[0], line[1]])].append(line[2])
|
||||
head_filter_entities["\t".join([line[2], line[1]])].append(line[0])
|
||||
|
||||
max_head_entities = max(len(_) for _ in head_filter_entities.values())
|
||||
max_tail_entities = max(len(_) for _ in tail_filter_entities.values())
|
||||
|
||||
# use bce loss, ignore the mlm
|
||||
if set_type == "train" and args.bce:
|
||||
lines = []
|
||||
for k, v in tail_filter_entities.items():
|
||||
h, r = k.split('\t')
|
||||
t = v[0]
|
||||
lines.append([h, r, t])
|
||||
for k, v in head_filter_entities.items():
|
||||
t, r = k.split('\t')
|
||||
h = v[0]
|
||||
lines.append([h, r, t])
|
||||
|
||||
|
||||
# for training , select each entity as for get mask embedding.
|
||||
if args.pretrain:
|
||||
rel = list(rel2text.keys())[0]
|
||||
lines = []
|
||||
for k in ent2text.keys():
|
||||
lines.append([k, rel, k])
|
||||
|
||||
print(f"max number of filter entities : {max_head_entities} {max_tail_entities}")
|
||||
# 把子图信息加入到filter_init中（初始化为文件夹，及固定子图），设置为全局变量，solve中调用
|
||||
from os import cpu_count
|
||||
threads = min(1, cpu_count())
|
||||
filter_init(head_filter_entities, tail_filter_entities,ent2text, rel2text, ent2id, ent2token, rel2id, masked_head_neighbor, masked_tail_neighbor, rel2token
|
||||
)
|
||||
|
||||
if hasattr(args, "faiss_init") and args.faiss_init:
|
||||
annotate_ = partial(
|
||||
solve_get_knowledge_store,
|
||||
pretrain=self.args.pretrain
|
||||
)
|
||||
else:
|
||||
annotate_ = partial(
|
||||
solve,
|
||||
pretrain=self.args.pretrain,
|
||||
max_triplet=self.args.max_triplet
|
||||
)
|
||||
examples = list(
|
||||
tqdm(
|
||||
map(annotate_, lines),
|
||||
total=len(lines),
|
||||
desc="convert text to examples"
|
||||
)
|
||||
)
|
||||
|
||||
tmp_examples = []
|
||||
for e in examples:
|
||||
for ee in e:
|
||||
tmp_examples.append(ee)
|
||||
examples = tmp_examples
|
||||
# delete vars
|
||||
del head_filter_entities, tail_filter_entities, ent2text, rel2text, ent2id, ent2token, rel2id
|
||||
return examples
|
||||
|
||||
class Verbalizer(object):
|
||||
def __init__(self, args):
|
||||
if "WN18RR" in args.data_dir:
|
||||
self.mode = "WN18RR"
|
||||
elif "FB15k" in args.data_dir:
|
||||
self.mode = "FB15k"
|
||||
elif "umls" in args.data_dir:
|
||||
self.mode = "umls"
|
||||
elif "codexs" in args.data_dir:
|
||||
self.mode = "codexs"
|
||||
elif "FB13" in args.data_dir:
|
||||
self.mode = "FB13"
|
||||
elif "WN11" in args.data_dir:
|
||||
self.mode = "WN11"
|
||||
|
||||
|
||||
def _convert(self, head, relation, tail):
|
||||
if self.mode == "umls":
|
||||
return f"The {relation} {head} is "
|
||||
|
||||
return f"{head} {relation}"
|
||||
|
||||
|
||||
class KGCDataset(Dataset):
|
||||
def __init__(self, features):
|
||||
self.features = features
|
||||
|
||||
def __getitem__(self, index):
|
||||
return self.features[index]
|
||||
|
||||
def __len__(self):
|
||||
return len(self.features)
|
||||
|
||||
def convert_examples_to_features_init(tokenizer_for_convert):
|
||||
global tokenizer
|
||||
tokenizer = tokenizer_for_convert
|
||||
|
||||
def convert_examples_to_features(example, max_seq_length, mode, pretrain=1):
|
||||
"""Loads a data file into a list of `InputBatch`s."""
|
||||
text_a = " ".join(example.text_a.split()[:128])
|
||||
text_b = " ".join(example.text_b.split()[:128])
|
||||
text_c = " ".join(example.text_c.split()[:128])
|
||||
|
||||
if pretrain:
|
||||
input_text_a = text_a
|
||||
input_text_b = text_b
|
||||
else:
|
||||
input_text_a = " ".join([text_a, text_b])
|
||||
input_text_b = text_c
|
||||
|
||||
|
||||
inputs = tokenizer(
|
||||
input_text_a,
|
||||
input_text_b,
|
||||
truncation="longest_first",
|
||||
max_length=max_seq_length,
|
||||
padding="longest",
|
||||
add_special_tokens=True,
|
||||
)
|
||||
# assert tokenizer.mask_token_id in inputs.input_ids, "mask token must in input"
|
||||
|
||||
features = asdict(InputFeatures(input_ids=inputs["input_ids"],
|
||||
attention_mask=inputs['attention_mask'],
|
||||
labels=torch.tensor(example.label),
|
||||
label=torch.tensor(example.real_label)
|
||||
)
|
||||
)
|
||||
return features
|
||||
|
||||
|
||||
def _truncate_seq_pair(tokens_a, tokens_b, max_length):
|
||||
"""Truncates a sequence pair in place to the maximum length."""
|
||||
|
||||
# This is a simple heuristic which will always truncate the longer sequence
|
||||
# one token at a time. This makes more sense than truncating an equal percent
|
||||
# of tokens from each, since if one sequence is very short then each token
|
||||
# that's truncated likely contains more information than a longer sequence.
|
||||
while True:
|
||||
total_length = len(tokens_a) + len(tokens_b)
|
||||
if total_length <= max_length:
|
||||
break
|
||||
if len(tokens_a) > len(tokens_b):
|
||||
tokens_a.pop()
|
||||
else:
|
||||
tokens_b.pop()
|
||||
|
||||
def _truncate_seq_triple(tokens_a, tokens_b, tokens_c, max_length):
|
||||
"""Truncates a sequence triple in place to the maximum length."""
|
||||
|
||||
# This is a simple heuristic which will always truncate the longer sequence
|
||||
# one token at a time. This makes more sense than truncating an equal percent
|
||||
# of tokens from each, since if one sequence is very short then each token
|
||||
# that's truncated likely contains more information than a longer sequence.
|
||||
while True:
|
||||
total_length = len(tokens_a) + len(tokens_b) + len(tokens_c)
|
||||
if total_length <= max_length:
|
||||
break
|
||||
if len(tokens_a) > len(tokens_b) and len(tokens_a) > len(tokens_c):
|
||||
tokens_a.pop()
|
||||
elif len(tokens_b) > len(tokens_a) and len(tokens_b) > len(tokens_c):
|
||||
tokens_b.pop()
|
||||
elif len(tokens_c) > len(tokens_a) and len(tokens_c) > len(tokens_b):
|
||||
tokens_c.pop()
|
||||
else:
|
||||
tokens_c.pop()
|
||||
|
||||
|
||||
@cache_results(_cache_fp="./dataset")
|
||||
def get_dataset(args, processor, label_list, tokenizer, mode):
|
||||
|
||||
assert mode in ["train", "dev", "test"], "mode must be in train dev test!"
|
||||
|
||||
# use training data to construct the entity embedding
|
||||
combine_train_and_test = False
|
||||
if args.faiss_init and mode == "test" and not args.pretrain:
|
||||
mode = "train"
|
||||
if "ind" in args.data_dir: combine_train_and_test = True
|
||||
else:
|
||||
pass
|
||||
|
||||
if mode == "train":
|
||||
train_examples = processor.get_train_examples(args.data_dir)
|
||||
elif mode == "dev":
|
||||
train_examples = processor.get_dev_examples(args.data_dir)
|
||||
else:
|
||||
train_examples = processor.get_test_examples(args.data_dir)
|
||||
|
||||
if combine_train_and_test:
|
||||
logger.info("use all the dataset for getting the entity mask embedding in pretraining pretraining")
|
||||
logger.info("use all the dataset for getting the entity mask embedding in pretraining pretraining")
|
||||
train_examples = processor.get_test_examples(args.data_dir) + processor.get_train_examples(args.data_dir) + processor.get_dev_examples(args.data_dir)
|
||||
|
||||
from os import cpu_count
|
||||
with open(os.path.join(args.data_dir, f"examples_{mode}.txt"), 'w') as file:
|
||||
for line in train_examples:
|
||||
d = {}
|
||||
d.update(line.__dict__)
|
||||
file.write(json.dumps(d) + '\n')
|
||||
|
||||
# 这里应该不需要重新from_pretrain，必须沿用加入token的
|
||||
tokenizer = AutoTokenizer.from_pretrained(args.model_name_or_path, use_fast=False)
|
||||
|
||||
features = []
|
||||
|
||||
file_inputs = [os.path.join(args.data_dir, f"examples_{mode}.txt")]
|
||||
file_outputs = [os.path.join(args.data_dir, f"features_{mode}.txt")]
|
||||
|
||||
with contextlib.ExitStack() as stack:
|
||||
inputs = [
|
||||
stack.enter_context(open(input, "r", encoding="utf-8"))
|
||||
if input != "-" else sys.stdin
|
||||
for input in file_inputs
|
||||
]
|
||||
outputs = [
|
||||
stack.enter_context(open(output, "w", encoding="utf-8"))
|
||||
if output != "-" else sys.stdout
|
||||
for output in file_outputs
|
||||
]
|
||||
|
||||
encoder = MultiprocessingEncoder(tokenizer, args)
|
||||
pool = Pool(16, initializer=encoder.initializer)
|
||||
encoder.initializer()
|
||||
encoded_lines = pool.imap(encoder.encode_lines, zip(*inputs), 1000)
|
||||
# encoded_lines = map(encoder.encode_lines, zip(*inputs))
|
||||
|
||||
stats = Counter()
|
||||
for i, (filt, enc_lines) in tqdm(enumerate(encoded_lines, start=1), total=len(train_examples)):
|
||||
if filt == "PASS":
|
||||
for enc_line, output_h in zip(enc_lines, outputs):
|
||||
features.append(eval(enc_line))
|
||||
# features.append(enc_line)
|
||||
# print(enc_line, file=output_h)
|
||||
else:
|
||||
stats["num_filtered_" + filt] += 1
|
||||
|
||||
for k, v in stats.most_common():
|
||||
print("[{}] filtered {} lines".format(k, v), file=sys.stderr)
|
||||
|
||||
for f_id, f in enumerate(features):
|
||||
en = features[f_id].pop("en")
|
||||
rel = features[f_id].pop("rel")
|
||||
graph = features[f_id].pop("graph")
|
||||
real_label = f['label']
|
||||
features[f_id]['distance_attention'] = torch.Tensor(features[f_id]['distance_attention'])
|
||||
|
||||
cnt = 0
|
||||
cnt_2 = 0
|
||||
if not isinstance(en, list): break
|
||||
|
||||
pos = 0
|
||||
for i,t in enumerate(f['input_ids']):
|
||||
if t == tokenizer.pad_token_id:
|
||||
features[f_id]['input_ids'][i] = en[cnt] + len(tokenizer)
|
||||
cnt += 1
|
||||
if t == tokenizer.unk_token_id:
|
||||
features[f_id]['input_ids'][i] = graph[cnt_2] + len(tokenizer)
|
||||
cnt_2 += 1
|
||||
if features[f_id]['input_ids'][i] == real_label + len(tokenizer):
|
||||
pos = i
|
||||
if cnt_2 == len(graph) and cnt == len(en): break
|
||||
# 如果等于UNK， pop出图节点list，然后替换
|
||||
assert not (args.faiss_init and pos == 0)
|
||||
features[f_id]['pos'] = pos
|
||||
|
||||
# for i,t in enumerate(f['input_ids']):
|
||||
# if t == tokenizer.pad_token_id:
|
||||
# features[f_id]['input_ids'][i] = rel + len(tokenizer) + num_entities
|
||||
# break
|
||||
|
||||
|
||||
|
||||
features = KGCDataset(features)
|
||||
return features
|
||||
|
||||
|
||||
class MultiprocessingEncoder(object):
|
||||
def __init__(self, tokenizer, args):
|
||||
self.tokenizer = tokenizer
|
||||
self.pretrain = args.pretrain
|
||||
self.max_seq_length = args.max_seq_length
|
||||
|
||||
def initializer(self):
|
||||
global bpe
|
||||
bpe = self.tokenizer
|
||||
|
||||
def encode(self, line):
|
||||
global bpe
|
||||
ids = bpe.encode(line)
|
||||
return list(map(str, ids))
|
||||
|
||||
def decode(self, tokens):
|
||||
global bpe
|
||||
return bpe.decode(tokens)
|
||||
|
||||
def encode_lines(self, lines):
|
||||
"""
|
||||
Encode a set of lines. All lines will be encoded together.
|
||||
"""
|
||||
enc_lines = []
|
||||
for line in lines:
|
||||
line = line.strip()
|
||||
if len(line) == 0:
|
||||
return ["EMPTY", None]
|
||||
# enc_lines.append(" ".join(tokens))
|
||||
enc_lines.append(json.dumps(self.convert_examples_to_features(example=eval(line))))
|
||||
# enc_lines.append(" ")
|
||||
# enc_lines.append("123")
|
||||
return ["PASS", enc_lines]
|
||||
|
||||
def decode_lines(self, lines):
|
||||
dec_lines = []
|
||||
for line in lines:
|
||||
tokens = map(int, line.strip().split())
|
||||
dec_lines.append(self.decode(tokens))
|
||||
return ["PASS", dec_lines]
|
||||
|
||||
def convert_examples_to_features(self, example):
|
||||
pretrain = self.pretrain
|
||||
max_seq_length = self.max_seq_length
|
||||
global bpe
|
||||
"""Loads a data file into a list of `InputBatch`s."""
|
||||
# tokens_a = tokenizer.tokenize(example.text_a)
|
||||
# tokens_b = tokenizer.tokenize(example.text_b)
|
||||
# tokens_c = tokenizer.tokenize(example.text_c)
|
||||
|
||||
# _truncate_seq_triple(tokens_a, tokens_b, tokens_c, max_length= max_seq_length)
|
||||
# text_a = " ".join(example['text_a'].split()[:128])
|
||||
# text_b = " ".join(example['text_b'].split()[:128])
|
||||
# text_c = " ".join(example['text_c'].split()[:128])
|
||||
|
||||
text_a = example['text_a']
|
||||
text_b = example['text_b']
|
||||
text_c = example['text_c']
|
||||
text_d = example['text_d']
|
||||
graph_list = example['graph_inf']
|
||||
|
||||
if pretrain:
|
||||
# the des of xxx is [MASK] .
|
||||
input_text = f"The description of {text_a} is that {text_b} ."
|
||||
inputs = bpe(
|
||||
input_text,
|
||||
truncation="longest_first",
|
||||
max_length=max_seq_length,
|
||||
padding="longest",
|
||||
add_special_tokens=True,
|
||||
)
|
||||
else:
|
||||
if text_a == "[MASK]":
|
||||
input_text_a = " ".join([text_a, text_b])
|
||||
input_text_b = text_c
|
||||
origin_triplet = ["MASK"] + example['en']
|
||||
graph_seq = ["MASK"] + example['en'] + text_d
|
||||
else:
|
||||
input_text_a = text_a
|
||||
input_text_b = " ".join([text_b, text_c])
|
||||
origin_triplet = example['en'] + ["MASK"]
|
||||
graph_seq = example['en'] + ["MASK"] + text_d
|
||||
# 加入graph信息, 拼接等量[UNK]
|
||||
input_text_b = " ".join(["[CLS]", input_text_a, input_text_b, bpe.unk_token * len(text_d)])
|
||||
|
||||
inputs = bpe(
|
||||
input_text_b,
|
||||
truncation="longest_first",
|
||||
max_length=max_seq_length,
|
||||
padding="longest",
|
||||
add_special_tokens=False,
|
||||
)
|
||||
# assert bpe.mask_token_id in inputs.input_ids, "mask token must in input"
|
||||
|
||||
# graph_seq = input_text_b[] 把图结构信息读取出来
|
||||
# [CLS] [ENTITY_13258] [RELATION_68] [MASK] [ENTITY_4] [RELATION_127] [ENTITY_8] [RELATION_9] [ENTITY_9011] [ENTITY_12477] [PAD] [PAD]
|
||||
# 获取图结构信息
|
||||
# 首先在solve中加入一个存储所有子图三元组的临时存储变量
|
||||
# 在这里graph_information = example['graph']
|
||||
new_rel = set()
|
||||
new_rel.add(tuple((origin_triplet[0], origin_triplet[1])))
|
||||
new_rel.add(tuple((origin_triplet[1], origin_triplet[0])))
|
||||
new_rel.add(tuple((origin_triplet[1], origin_triplet[2])))
|
||||
new_rel.add(tuple((origin_triplet[2], origin_triplet[1])))
|
||||
for triplet in graph_list:
|
||||
rel1, rel2, rel3, rel4 = tuple((triplet[0], triplet[1])), tuple((triplet[1], triplet[2])), tuple((triplet[1], triplet[0])), tuple((triplet[2], triplet[1]))
|
||||
new_rel.add(rel1)
|
||||
new_rel.add(rel2)
|
||||
new_rel.add(rel3)
|
||||
new_rel.add(rel4)
|
||||
# 这里的三元组转换为new_rel
|
||||
KGid2Graphid_map = defaultdict(int)
|
||||
for i in range(len(graph_seq)):
|
||||
KGid2Graphid_map[graph_seq[i]] = i
|
||||
|
||||
N = len(graph_seq)
|
||||
adj = torch.zeros([N, N], dtype=torch.bool)
|
||||
for item in list(new_rel):
|
||||
adj[KGid2Graphid_map[item[0]], KGid2Graphid_map[item[1]]] = True
|
||||
shortest_path_result, _ = algos.floyd_warshall(adj.numpy())
|
||||
max_dist = np.amax(shortest_path_result)
|
||||
# [PAD]部分， [CLS]部分补全， [SEP]额外引入也当作[PAD]处理
|
||||
# 加上一个attention_bias, PAD部分设置为-inf，在送入model前，对其进行处理, 将其相加（让模型无法关注PAD）
|
||||
|
||||
# 加入attention到huggingface的BertForMaskedLM（这个可能需要再去查查）
|
||||
# attention_bias = torch.zero(N, N, dtype=torch.float)
|
||||
# attention_bias[torch.tensor(shortest_path_result == )]
|
||||
features = asdict(InputFeatures(input_ids=inputs["input_ids"],
|
||||
attention_mask=inputs['attention_mask'],
|
||||
labels=example['label'],
|
||||
label=example['real_label'],
|
||||
en=example['en_id'],
|
||||
rel=example['rel'],
|
||||
graph=example['text_d_id'],
|
||||
distance_attention = shortest_path_result.tolist(),
|
||||
)
|
||||
)
|
||||
return features
|
||||
661
data/umls/test.txt
Normal file
661
data/umls/test.txt
Normal file
@ -0,0 +1,661 @@
|
||||
steroid interacts_with eicosanoid
|
||||
clinical_attribute isa conceptual_entity
|
||||
body_location_or_region location_of physiologic_function
|
||||
neoplastic_process isa disease_or_syndrome
|
||||
carbohydrate affects molecular_function
|
||||
disease_or_syndrome affects organ_or_tissue_function
|
||||
substance issue_in occupation_or_discipline
|
||||
laboratory_or_test_result evaluation_of genetic_function
|
||||
chemical_viewed_functionally isa entity
|
||||
organophosphorus_compound ingredient_of clinical_drug
|
||||
mental_or_behavioral_dysfunction affects social_behavior
|
||||
human_caused_phenomenon_or_process result_of pathologic_function
|
||||
amino_acid_peptide_or_protein interacts_with antibiotic
|
||||
hormone affects experimental_model_of_disease
|
||||
antibiotic affects cell_function
|
||||
embryonic_structure part_of bird
|
||||
tissue produces organic_chemical
|
||||
genetic_function process_of organ_or_tissue_function
|
||||
congenital_abnormality part_of mammal
|
||||
inorganic_chemical causes cell_or_molecular_dysfunction
|
||||
receptor disrupts cell
|
||||
professional_society location_of laboratory_procedure
|
||||
organism_function co-occurs_with cell_function
|
||||
immunologic_factor causes cell_or_molecular_dysfunction
|
||||
vitamin affects neoplastic_process
|
||||
antibiotic complicates anatomical_abnormality
|
||||
quantitative_concept measurement_of physiologic_function
|
||||
pathologic_function affects biologic_function
|
||||
congenital_abnormality issue_in occupation_or_discipline
|
||||
tissue adjacent_to body_space_or_junction
|
||||
vitamin disrupts organ_or_tissue_function
|
||||
receptor isa substance
|
||||
mental_process isa organism_function
|
||||
vertebrate exhibits individual_behavior
|
||||
body_location_or_region location_of therapeutic_or_preventive_procedure
|
||||
physical_object issue_in biomedical_occupation_or_discipline
|
||||
inorganic_chemical affects cell_function
|
||||
neoplastic_process affects vertebrate
|
||||
cell_function affects mammal
|
||||
population_group uses medical_device
|
||||
human_caused_phenomenon_or_process result_of molecular_function
|
||||
pharmacologic_substance treats neoplastic_process
|
||||
embryonic_structure location_of cell_or_molecular_dysfunction
|
||||
experimental_model_of_disease result_of laboratory_procedure
|
||||
enzyme disrupts cell_function
|
||||
pathologic_function complicates injury_or_poisoning
|
||||
mental_or_behavioral_dysfunction degree_of disease_or_syndrome
|
||||
plant interacts_with animal
|
||||
disease_or_syndrome process_of pathologic_function
|
||||
pathologic_function result_of diagnostic_procedure
|
||||
anatomical_abnormality manifestation_of biologic_function
|
||||
laboratory_or_test_result manifestation_of pathologic_function
|
||||
fish issue_in biomedical_occupation_or_discipline
|
||||
carbohydrate affects cell_or_molecular_dysfunction
|
||||
biologic_function affects virus
|
||||
mental_process precedes cell_function
|
||||
experimental_model_of_disease occurs_in mental_or_behavioral_dysfunction
|
||||
congenital_abnormality part_of bacterium
|
||||
human_caused_phenomenon_or_process result_of physiologic_function
|
||||
cell location_of therapeutic_or_preventive_procedure
|
||||
experimental_model_of_disease process_of natural_phenomenon_or_process
|
||||
neoplastic_process result_of phenomenon_or_process
|
||||
neuroreactive_substance_or_biogenic_amine affects organism_function
|
||||
mental_or_behavioral_dysfunction process_of archaeon
|
||||
congenital_abnormality part_of virus
|
||||
pathologic_function manifestation_of genetic_function
|
||||
biologically_active_substance causes mental_or_behavioral_dysfunction
|
||||
pharmacologic_substance treats disease_or_syndrome
|
||||
body_space_or_junction location_of cell_function
|
||||
genetic_function affects virus
|
||||
acquired_abnormality result_of diagnostic_procedure
|
||||
physiologic_function affects archaeon
|
||||
cell_component location_of pathologic_function
|
||||
molecular_biology_research_technique measures chemical_viewed_functionally
|
||||
molecular_function result_of human_caused_phenomenon_or_process
|
||||
professional_or_occupational_group uses manufactured_object
|
||||
receptor disrupts molecular_function
|
||||
organ_or_tissue_function process_of biologic_function
|
||||
molecular_biology_research_technique measures element_ion_or_isotope
|
||||
physiologic_function result_of experimental_model_of_disease
|
||||
physiologic_function produces biologically_active_substance
|
||||
fully_formed_anatomical_structure part_of amphibian
|
||||
enzyme complicates organism_function
|
||||
tissue location_of virus
|
||||
invertebrate isa animal
|
||||
mental_process co-occurs_with genetic_function
|
||||
anatomical_abnormality location_of bacterium
|
||||
fully_formed_anatomical_structure location_of cell_or_molecular_dysfunction
|
||||
organ_or_tissue_function co-occurs_with genetic_function
|
||||
physiologic_function result_of human_caused_phenomenon_or_process
|
||||
molecular_function result_of cell_or_molecular_dysfunction
|
||||
diagnostic_procedure associated_with pathologic_function
|
||||
physiologic_function result_of neoplastic_process
|
||||
lipid interacts_with pharmacologic_substance
|
||||
cell_component produces receptor
|
||||
physiologic_function result_of congenital_abnormality
|
||||
age_group performs machine_activity
|
||||
congenital_abnormality associated_with organism_attribute
|
||||
laboratory_procedure analyzes amino_acid_peptide_or_protein
|
||||
vitamin affects mental_process
|
||||
cell_component part_of organism
|
||||
classification isa conceptual_entity
|
||||
organism_function result_of pathologic_function
|
||||
organism_function produces vitamin
|
||||
laboratory_procedure diagnoses mental_or_behavioral_dysfunction
|
||||
carbohydrate affects pathologic_function
|
||||
cell_component isa entity
|
||||
pathologic_function affects organism
|
||||
mental_process affects bacterium
|
||||
laboratory_or_test_result indicates organ_or_tissue_function
|
||||
tissue produces body_substance
|
||||
cell_component part_of body_part_organ_or_organ_component
|
||||
molecular_function affects mental_or_behavioral_dysfunction
|
||||
carbohydrate interacts_with immunologic_factor
|
||||
daily_or_recreational_activity associated_with acquired_abnormality
|
||||
molecular_function result_of disease_or_syndrome
|
||||
neoplastic_process occurs_in injury_or_poisoning
|
||||
fully_formed_anatomical_structure part_of archaeon
|
||||
carbohydrate affects mental_process
|
||||
element_ion_or_isotope interacts_with hazardous_or_poisonous_substance
|
||||
injury_or_poisoning disrupts molecular_function
|
||||
professional_or_occupational_group interacts_with population_group
|
||||
mental_or_behavioral_dysfunction affects archaeon
|
||||
organic_chemical affects neoplastic_process
|
||||
substance causes disease_or_syndrome
|
||||
biologically_active_substance causes disease_or_syndrome
|
||||
injury_or_poisoning disrupts tissue
|
||||
pathologic_function issue_in occupation_or_discipline
|
||||
mental_or_behavioral_dysfunction process_of reptile
|
||||
acquired_abnormality manifestation_of pathologic_function
|
||||
element_ion_or_isotope issue_in biomedical_occupation_or_discipline
|
||||
behavior associated_with age_group
|
||||
disease_or_syndrome complicates cell_or_molecular_dysfunction
|
||||
fully_formed_anatomical_structure produces receptor
|
||||
chemical causes injury_or_poisoning
|
||||
mental_or_behavioral_dysfunction affects reptile
|
||||
biologic_function affects organism_function
|
||||
antibiotic interacts_with neuroreactive_substance_or_biogenic_amine
|
||||
biologically_active_substance affects mental_or_behavioral_dysfunction
|
||||
laboratory_procedure assesses_effect_of genetic_function
|
||||
research_activity measures amino_acid_peptide_or_protein
|
||||
disease_or_syndrome affects cell_or_molecular_dysfunction
|
||||
pathologic_function result_of disease_or_syndrome
|
||||
disease_or_syndrome occurs_in mental_or_behavioral_dysfunction
|
||||
social_behavior associated_with patient_or_disabled_group
|
||||
antibiotic diagnoses mental_or_behavioral_dysfunction
|
||||
pathologic_function result_of organism_function
|
||||
plant interacts_with reptile
|
||||
mental_or_behavioral_dysfunction affects amphibian
|
||||
sign_or_symptom diagnoses mental_or_behavioral_dysfunction
|
||||
biologic_function result_of mental_or_behavioral_dysfunction
|
||||
biologic_function affects cell_or_molecular_dysfunction
|
||||
anatomical_abnormality part_of vertebrate
|
||||
family_group interacts_with group
|
||||
experimental_model_of_disease process_of fish
|
||||
mental_or_behavioral_dysfunction affects natural_phenomenon_or_process
|
||||
organism_function affects alga
|
||||
cell_component location_of body_space_or_junction
|
||||
body_part_organ_or_organ_component location_of genetic_function
|
||||
chemical affects genetic_function
|
||||
chemical_viewed_functionally affects physiologic_function
|
||||
language issue_in biomedical_occupation_or_discipline
|
||||
body_part_organ_or_organ_component location_of organ_or_tissue_function
|
||||
research_activity isa occupational_activity
|
||||
diagnostic_procedure analyzes hazardous_or_poisonous_substance
|
||||
experimental_model_of_disease occurs_in group
|
||||
nucleic_acid_nucleoside_or_nucleotide isa entity
|
||||
diagnostic_procedure associated_with congenital_abnormality
|
||||
occupational_activity associated_with cell_or_molecular_dysfunction
|
||||
organ_or_tissue_function result_of acquired_abnormality
|
||||
molecular_function affects cell_function
|
||||
chemical_viewed_structurally ingredient_of clinical_drug
|
||||
mental_or_behavioral_dysfunction result_of behavior
|
||||
chemical_viewed_structurally interacts_with carbohydrate
|
||||
cell_function affects neoplastic_process
|
||||
pathologic_function occurs_in mental_or_behavioral_dysfunction
|
||||
family_group performs therapeutic_or_preventive_procedure
|
||||
family_group produces research_device
|
||||
amino_acid_peptide_or_protein affects mental_process
|
||||
hormone complicates biologic_function
|
||||
anatomical_abnormality result_of health_care_activity
|
||||
organism_function process_of biologic_function
|
||||
immunologic_factor complicates disease_or_syndrome
|
||||
nucleotide_sequence property_of nucleic_acid_nucleoside_or_nucleotide
|
||||
organization location_of occupational_activity
|
||||
clinical_attribute result_of genetic_function
|
||||
vitamin causes anatomical_abnormality
|
||||
mental_or_behavioral_dysfunction affects organ_or_tissue_function
|
||||
neoplastic_process result_of mental_or_behavioral_dysfunction
|
||||
body_part_organ_or_organ_component produces organic_chemical
|
||||
virus isa organism
|
||||
organ_or_tissue_function process_of physiologic_function
|
||||
individual_behavior associated_with occupation_or_discipline
|
||||
hazardous_or_poisonous_substance affects disease_or_syndrome
|
||||
cell_or_molecular_dysfunction affects physiologic_function
|
||||
hormone disrupts tissue
|
||||
molecular_function affects animal
|
||||
physiologic_function affects molecular_function
|
||||
biologic_function affects physiologic_function
|
||||
laboratory_or_test_result indicates mental_process
|
||||
chemical_viewed_structurally affects organ_or_tissue_function
|
||||
cell_function result_of disease_or_syndrome
|
||||
amino_acid_peptide_or_protein affects biologic_function
|
||||
experimental_model_of_disease affects biologic_function
|
||||
biomedical_or_dental_material affects biologic_function
|
||||
molecular_biology_research_technique measures amino_acid_peptide_or_protein
|
||||
experimental_model_of_disease affects bacterium
|
||||
antibiotic affects organ_or_tissue_function
|
||||
human isa mammal
|
||||
population_group performs daily_or_recreational_activity
|
||||
cell_component conceptual_part_of body_system
|
||||
cell part_of reptile
|
||||
organ_or_tissue_function affects human
|
||||
indicator_reagent_or_diagnostic_aid interacts_with chemical
|
||||
cell_or_molecular_dysfunction result_of organism_function
|
||||
molecular_biology_research_technique measures eicosanoid
|
||||
molecular_biology_research_technique measures natural_phenomenon_or_process
|
||||
organism_attribute result_of disease_or_syndrome
|
||||
pharmacologic_substance treats injury_or_poisoning
|
||||
genetic_function affects biologic_function
|
||||
group exhibits individual_behavior
|
||||
human_caused_phenomenon_or_process result_of phenomenon_or_process
|
||||
antibiotic affects genetic_function
|
||||
hormone interacts_with enzyme
|
||||
pathologic_function process_of archaeon
|
||||
bird interacts_with mammal
|
||||
neuroreactive_substance_or_biogenic_amine disrupts organ_or_tissue_function
|
||||
carbohydrate causes cell_or_molecular_dysfunction
|
||||
cell_function affects disease_or_syndrome
|
||||
cell part_of fungus
|
||||
organism_function process_of human
|
||||
receptor complicates mental_or_behavioral_dysfunction
|
||||
genetic_function isa molecular_function
|
||||
mental_or_behavioral_dysfunction degree_of cell_or_molecular_dysfunction
|
||||
group_attribute property_of family_group
|
||||
pharmacologic_substance diagnoses experimental_model_of_disease
|
||||
pathologic_function affects alga
|
||||
tissue location_of biologic_function
|
||||
organism_function co-occurs_with mental_process
|
||||
occupational_activity associated_with neoplastic_process
|
||||
indicator_reagent_or_diagnostic_aid affects genetic_function
|
||||
carbohydrate interacts_with biomedical_or_dental_material
|
||||
organism_function occurs_in temporal_concept
|
||||
inorganic_chemical causes anatomical_abnormality
|
||||
cell_or_molecular_dysfunction affects organism_function
|
||||
amphibian exhibits social_behavior
|
||||
anatomical_structure part_of alga
|
||||
lipid isa entity
|
||||
cell_or_molecular_dysfunction result_of disease_or_syndrome
|
||||
social_behavior associated_with professional_or_occupational_group
|
||||
cell produces hormone
|
||||
invertebrate isa entity
|
||||
organic_chemical causes cell_or_molecular_dysfunction
|
||||
acquired_abnormality result_of human_caused_phenomenon_or_process
|
||||
pathologic_function manifestation_of disease_or_syndrome
|
||||
chemical_viewed_functionally issue_in occupation_or_discipline
|
||||
experimental_model_of_disease co-occurs_with anatomical_abnormality
|
||||
laboratory_procedure assesses_effect_of element_ion_or_isotope
|
||||
diagnostic_procedure measures cell_function
|
||||
chemical_viewed_structurally issue_in occupation_or_discipline
|
||||
genetic_function affects disease_or_syndrome
|
||||
laboratory_or_test_result co-occurs_with sign_or_symptom
|
||||
amino_acid_peptide_or_protein interacts_with chemical_viewed_functionally
|
||||
cell part_of bacterium
|
||||
cell_function affects clinical_attribute
|
||||
fully_formed_anatomical_structure part_of plant
|
||||
chemical_viewed_structurally interacts_with lipid
|
||||
molecular_biology_research_technique measures molecular_function
|
||||
fungus interacts_with organism
|
||||
enzyme interacts_with vitamin
|
||||
congenital_abnormality manifestation_of mental_or_behavioral_dysfunction
|
||||
therapeutic_or_preventive_procedure complicates pathologic_function
|
||||
chemical affects organ_or_tissue_function
|
||||
virus location_of hormone
|
||||
organ_or_tissue_function produces hormone
|
||||
alga location_of neuroreactive_substance_or_biogenic_amine
|
||||
laboratory_procedure affects organ_or_tissue_function
|
||||
pathologic_function process_of invertebrate
|
||||
manufactured_object causes cell_or_molecular_dysfunction
|
||||
neoplastic_process affects rickettsia_or_chlamydia
|
||||
cell_or_molecular_dysfunction result_of acquired_abnormality
|
||||
genetic_function affects plant
|
||||
alga isa physical_object
|
||||
family_group performs laboratory_procedure
|
||||
disease_or_syndrome degree_of cell_or_molecular_dysfunction
|
||||
reptile exhibits social_behavior
|
||||
therapeutic_or_preventive_procedure affects patient_or_disabled_group
|
||||
qualitative_concept evaluation_of individual_behavior
|
||||
population_group uses regulation_or_law
|
||||
antibiotic causes cell_or_molecular_dysfunction
|
||||
cell_or_molecular_dysfunction occurs_in mental_or_behavioral_dysfunction
|
||||
acquired_abnormality manifestation_of genetic_function
|
||||
bacterium isa entity
|
||||
experimental_model_of_disease occurs_in age_group
|
||||
immunologic_factor causes congenital_abnormality
|
||||
laboratory_procedure measures pharmacologic_substance
|
||||
disease_or_syndrome affects fish
|
||||
biologic_function result_of neoplastic_process
|
||||
therapeutic_or_preventive_procedure associated_with acquired_abnormality
|
||||
cell produces vitamin
|
||||
mental_process process_of vertebrate
|
||||
mental_process result_of neoplastic_process
|
||||
diagnostic_procedure diagnoses cell_or_molecular_dysfunction
|
||||
rickettsia_or_chlamydia location_of vitamin
|
||||
neoplastic_process manifestation_of pathologic_function
|
||||
disease_or_syndrome precedes neoplastic_process
|
||||
physiologic_function result_of natural_phenomenon_or_process
|
||||
laboratory_or_test_result measurement_of food
|
||||
diagnostic_procedure assesses_effect_of element_ion_or_isotope
|
||||
vitamin causes cell_or_molecular_dysfunction
|
||||
carbohydrate_sequence isa idea_or_concept
|
||||
human_caused_phenomenon_or_process result_of injury_or_poisoning
|
||||
element_ion_or_isotope causes cell_or_molecular_dysfunction
|
||||
organic_chemical causes congenital_abnormality
|
||||
human_caused_phenomenon_or_process result_of experimental_model_of_disease
|
||||
experimental_model_of_disease complicates mental_or_behavioral_dysfunction
|
||||
organ_or_tissue_function isa natural_phenomenon_or_process
|
||||
nucleotide_sequence isa molecular_sequence
|
||||
physiologic_function affects fungus
|
||||
experimental_model_of_disease isa phenomenon_or_process
|
||||
cell_or_molecular_dysfunction manifestation_of injury_or_poisoning
|
||||
clinical_drug causes acquired_abnormality
|
||||
cell_component location_of genetic_function
|
||||
occupational_activity associated_with disease_or_syndrome
|
||||
laboratory_or_test_result associated_with anatomical_abnormality
|
||||
age_group performs social_behavior
|
||||
fully_formed_anatomical_structure location_of physiologic_function
|
||||
hormone interacts_with vitamin
|
||||
molecular_function precedes organism_function
|
||||
human_caused_phenomenon_or_process isa event
|
||||
professional_or_occupational_group performs diagnostic_procedure
|
||||
disease_or_syndrome co-occurs_with injury_or_poisoning
|
||||
mental_process produces biologically_active_substance
|
||||
molecular_function produces hormone
|
||||
neoplastic_process complicates congenital_abnormality
|
||||
neoplastic_process result_of mental_process
|
||||
eicosanoid issue_in biomedical_occupation_or_discipline
|
||||
health_care_related_organization isa entity
|
||||
cell_function isa biologic_function
|
||||
diagnostic_procedure analyzes pharmacologic_substance
|
||||
immunologic_factor complicates genetic_function
|
||||
physiologic_function precedes genetic_function
|
||||
immunologic_factor complicates physiologic_function
|
||||
mental_or_behavioral_dysfunction process_of mammal
|
||||
immunologic_factor indicates neoplastic_process
|
||||
neoplastic_process process_of genetic_function
|
||||
biologic_function affects fish
|
||||
organ_or_tissue_function affects bird
|
||||
mental_or_behavioral_dysfunction result_of environmental_effect_of_humans
|
||||
hazardous_or_poisonous_substance complicates neoplastic_process
|
||||
cell_or_molecular_dysfunction result_of social_behavior
|
||||
experimental_model_of_disease result_of human_caused_phenomenon_or_process
|
||||
element_ion_or_isotope interacts_with vitamin
|
||||
drug_delivery_device causes injury_or_poisoning
|
||||
fully_formed_anatomical_structure location_of fungus
|
||||
fully_formed_anatomical_structure location_of bacterium
|
||||
natural_phenomenon_or_process result_of disease_or_syndrome
|
||||
enzyme complicates experimental_model_of_disease
|
||||
individual_behavior manifestation_of mental_or_behavioral_dysfunction
|
||||
geographic_area isa idea_or_concept
|
||||
tissue isa fully_formed_anatomical_structure
|
||||
sign_or_symptom diagnoses experimental_model_of_disease
|
||||
educational_activity associated_with pathologic_function
|
||||
receptor affects biologic_function
|
||||
organ_or_tissue_function co-occurs_with physiologic_function
|
||||
mental_or_behavioral_dysfunction produces vitamin
|
||||
experimental_model_of_disease result_of physiologic_function
|
||||
hormone complicates physiologic_function
|
||||
self_help_or_relief_organization carries_out educational_activity
|
||||
environmental_effect_of_humans isa event
|
||||
chemical causes disease_or_syndrome
|
||||
diagnostic_procedure diagnoses congenital_abnormality
|
||||
cell_component part_of human
|
||||
experimental_model_of_disease result_of health_care_activity
|
||||
laboratory_or_test_result manifestation_of experimental_model_of_disease
|
||||
organism_attribute measurement_of mental_process
|
||||
cell_function affects genetic_function
|
||||
anatomical_structure part_of plant
|
||||
natural_phenomenon_or_process result_of pathologic_function
|
||||
congenital_abnormality result_of experimental_model_of_disease
|
||||
organism_function produces receptor
|
||||
food causes neoplastic_process
|
||||
hormone affects genetic_function
|
||||
diagnostic_procedure issue_in biomedical_occupation_or_discipline
|
||||
organ_or_tissue_function process_of mental_or_behavioral_dysfunction
|
||||
bird interacts_with archaeon
|
||||
laboratory_procedure analyzes organophosphorus_compound
|
||||
animal interacts_with organism
|
||||
laboratory_procedure assesses_effect_of disease_or_syndrome
|
||||
plant interacts_with alga
|
||||
therapeutic_or_preventive_procedure prevents neoplastic_process
|
||||
congenital_abnormality complicates anatomical_abnormality
|
||||
antibiotic disrupts organism_function
|
||||
age_group performs daily_or_recreational_activity
|
||||
gene_or_genome part_of plant
|
||||
amino_acid_peptide_or_protein interacts_with neuroreactive_substance_or_biogenic_amine
|
||||
pharmacologic_substance causes pathologic_function
|
||||
lipid issue_in occupation_or_discipline
|
||||
research_device causes anatomical_abnormality
|
||||
disease_or_syndrome process_of alga
|
||||
anatomical_abnormality result_of cell_function
|
||||
antibiotic treats experimental_model_of_disease
|
||||
antibiotic complicates mental_process
|
||||
injury_or_poisoning result_of cell_function
|
||||
physiologic_function precedes organ_or_tissue_function
|
||||
genetic_function result_of human_caused_phenomenon_or_process
|
||||
quantitative_concept measurement_of mental_process
|
||||
fungus causes pathologic_function
|
||||
rickettsia_or_chlamydia location_of immunologic_factor
|
||||
eicosanoid interacts_with element_ion_or_isotope
|
||||
inorganic_chemical causes neoplastic_process
|
||||
anatomical_structure issue_in biomedical_occupation_or_discipline
|
||||
immunologic_factor complicates injury_or_poisoning
|
||||
drug_delivery_device treats injury_or_poisoning
|
||||
research_device isa entity
|
||||
biologically_active_substance interacts_with neuroreactive_substance_or_biogenic_amine
|
||||
organophosphorus_compound interacts_with biologically_active_substance
|
||||
molecular_function affects amphibian
|
||||
mental_or_behavioral_dysfunction co-occurs_with injury_or_poisoning
|
||||
neoplastic_process manifestation_of experimental_model_of_disease
|
||||
bacterium location_of biologically_active_substance
|
||||
organic_chemical interacts_with biomedical_or_dental_material
|
||||
physiologic_function affects natural_phenomenon_or_process
|
||||
laboratory_procedure isa health_care_activity
|
||||
neoplastic_process complicates anatomical_abnormality
|
||||
anatomical_abnormality affects vertebrate
|
||||
clinical_attribute manifestation_of organ_or_tissue_function
|
||||
embryonic_structure part_of fungus
|
||||
inorganic_chemical interacts_with enzyme
|
||||
mental_or_behavioral_dysfunction co-occurs_with experimental_model_of_disease
|
||||
enzyme complicates neoplastic_process
|
||||
sign_or_symptom manifestation_of organ_or_tissue_function
|
||||
organ_or_tissue_function co-occurs_with molecular_function
|
||||
age_group isa group
|
||||
steroid affects neoplastic_process
|
||||
age_group exhibits behavior
|
||||
disease_or_syndrome manifestation_of physiologic_function
|
||||
diagnostic_procedure isa event
|
||||
biologically_active_substance disrupts gene_or_genome
|
||||
anatomical_abnormality manifestation_of mental_process
|
||||
cell_function result_of physiologic_function
|
||||
mental_process process_of human
|
||||
chemical issue_in biomedical_occupation_or_discipline
|
||||
alga interacts_with human
|
||||
vitamin affects biologic_function
|
||||
fully_formed_anatomical_structure produces carbohydrate
|
||||
environmental_effect_of_humans result_of acquired_abnormality
|
||||
disease_or_syndrome result_of human_caused_phenomenon_or_process
|
||||
organic_chemical interacts_with steroid
|
||||
cell_or_molecular_dysfunction process_of natural_phenomenon_or_process
|
||||
anatomical_abnormality part_of animal
|
||||
diagnostic_procedure uses drug_delivery_device
|
||||
molecular_biology_research_technique method_of diagnostic_procedure
|
||||
biologically_active_substance causes injury_or_poisoning
|
||||
anatomical_abnormality affects plant
|
||||
molecular_function process_of invertebrate
|
||||
diagnostic_procedure measures pharmacologic_substance
|
||||
element_ion_or_isotope affects molecular_function
|
||||
mental_or_behavioral_dysfunction result_of neoplastic_process
|
||||
machine_activity isa activity
|
||||
nucleic_acid_nucleoside_or_nucleotide interacts_with hormone
|
||||
laboratory_procedure affects neoplastic_process
|
||||
biomedical_or_dental_material isa chemical
|
||||
pathologic_function affects animal
|
||||
receptor causes pathologic_function
|
||||
indicator_reagent_or_diagnostic_aid causes anatomical_abnormality
|
||||
neuroreactive_substance_or_biogenic_amine affects cell_or_molecular_dysfunction
|
||||
cell_function affects rickettsia_or_chlamydia
|
||||
embryonic_structure location_of virus
|
||||
therapeutic_or_preventive_procedure affects cell_function
|
||||
human interacts_with organism
|
||||
fungus causes disease_or_syndrome
|
||||
cell produces receptor
|
||||
population_group produces regulation_or_law
|
||||
family_group performs research_activity
|
||||
vitamin causes injury_or_poisoning
|
||||
molecular_sequence issue_in biomedical_occupation_or_discipline
|
||||
steroid issue_in biomedical_occupation_or_discipline
|
||||
bacterium interacts_with fish
|
||||
cell_function result_of mental_process
|
||||
organism_attribute property_of mammal
|
||||
anatomical_abnormality manifestation_of disease_or_syndrome
|
||||
cell_or_molecular_dysfunction result_of environmental_effect_of_humans
|
||||
physiologic_function affects mammal
|
||||
fully_formed_anatomical_structure part_of bird
|
||||
organic_chemical interacts_with hormone
|
||||
idea_or_concept issue_in occupation_or_discipline
|
||||
patient_or_disabled_group uses research_device
|
||||
receptor causes acquired_abnormality
|
||||
biologic_function result_of disease_or_syndrome
|
||||
biologically_active_substance interacts_with enzyme
|
||||
physiologic_function isa biologic_function
|
||||
antibiotic complicates cell_function
|
||||
hazardous_or_poisonous_substance disrupts mental_process
|
||||
pathologic_function precedes cell_or_molecular_dysfunction
|
||||
organism_attribute property_of organism
|
||||
organophosphorus_compound interacts_with carbohydrate
|
||||
bacterium location_of receptor
|
||||
organ_or_tissue_function result_of experimental_model_of_disease
|
||||
fully_formed_anatomical_structure location_of organism_function
|
||||
finding isa conceptual_entity
|
||||
congenital_abnormality isa entity
|
||||
tissue issue_in biomedical_occupation_or_discipline
|
||||
natural_phenomenon_or_process result_of neoplastic_process
|
||||
organism_attribute manifestation_of organ_or_tissue_function
|
||||
therapeutic_or_preventive_procedure complicates cell_function
|
||||
population_group produces medical_device
|
||||
antibiotic interacts_with biologically_active_substance
|
||||
antibiotic causes acquired_abnormality
|
||||
cell_function produces vitamin
|
||||
neoplastic_process affects physiologic_function
|
||||
environmental_effect_of_humans result_of mental_or_behavioral_dysfunction
|
||||
organ_or_tissue_function affects organism_function
|
||||
lipid affects pathologic_function
|
||||
laboratory_procedure affects mental_process
|
||||
biologically_active_substance disrupts cell_component
|
||||
finding manifestation_of organism_function
|
||||
organism_function affects bird
|
||||
genetic_function affects physiologic_function
|
||||
cell_function result_of genetic_function
|
||||
antibiotic affects physiologic_function
|
||||
organophosphorus_compound causes pathologic_function
|
||||
natural_phenomenon_or_process affects genetic_function
|
||||
neoplastic_process produces receptor
|
||||
laboratory_procedure measures biomedical_or_dental_material
|
||||
organism_attribute measurement_of molecular_function
|
||||
physiologic_function affects biologic_function
|
||||
experimental_model_of_disease result_of neoplastic_process
|
||||
alga interacts_with virus
|
||||
congenital_abnormality location_of fungus
|
||||
antibiotic diagnoses cell_or_molecular_dysfunction
|
||||
diagnostic_procedure measures temporal_concept
|
||||
mental_or_behavioral_dysfunction result_of biologic_function
|
||||
pharmacologic_substance complicates biologic_function
|
||||
pharmacologic_substance disrupts organism_function
|
||||
anatomical_abnormality result_of injury_or_poisoning
|
||||
fully_formed_anatomical_structure location_of molecular_function
|
||||
nucleic_acid_nucleoside_or_nucleotide interacts_with antibiotic
|
||||
neuroreactive_substance_or_biogenic_amine isa biologically_active_substance
|
||||
experimental_model_of_disease process_of bacterium
|
||||
neuroreactive_substance_or_biogenic_amine interacts_with chemical
|
||||
cell_or_molecular_dysfunction affects bird
|
||||
laboratory_or_test_result isa conceptual_entity
|
||||
pathologic_function associated_with organism_attribute
|
||||
acquired_abnormality co-occurs_with injury_or_poisoning
|
||||
professional_or_occupational_group uses drug_delivery_device
|
||||
professional_or_occupational_group diagnoses experimental_model_of_disease
|
||||
cell_or_molecular_dysfunction degree_of neoplastic_process
|
||||
neoplastic_process issue_in biomedical_occupation_or_discipline
|
||||
disease_or_syndrome result_of mental_process
|
||||
neoplastic_process process_of bird
|
||||
pathologic_function result_of anatomical_abnormality
|
||||
congenital_abnormality manifestation_of disease_or_syndrome
|
||||
organism_attribute result_of neoplastic_process
|
||||
injury_or_poisoning issue_in occupation_or_discipline
|
||||
receptor causes mental_or_behavioral_dysfunction
|
||||
clinical_attribute property_of bacterium
|
||||
nucleic_acid_nucleoside_or_nucleotide affects experimental_model_of_disease
|
||||
lipid causes congenital_abnormality
|
||||
chemical_viewed_structurally interacts_with chemical_viewed_functionally
|
||||
antibiotic prevents pathologic_function
|
||||
eicosanoid isa organic_chemical
|
||||
biologically_active_substance disrupts organ_or_tissue_function
|
||||
organ_or_tissue_function affects genetic_function
|
||||
antibiotic affects neoplastic_process
|
||||
fully_formed_anatomical_structure location_of virus
|
||||
qualitative_concept evaluation_of activity
|
||||
embryonic_structure part_of cell
|
||||
enzyme disrupts tissue
|
||||
governmental_or_regulatory_activity associated_with disease_or_syndrome
|
||||
gene_or_genome location_of mental_process
|
||||
neoplastic_process process_of organism_function
|
||||
pharmacologic_substance issue_in biomedical_occupation_or_discipline
|
||||
receptor complicates disease_or_syndrome
|
||||
disease_or_syndrome process_of genetic_function
|
||||
anatomical_abnormality location_of virus
|
||||
embryonic_structure part_of vertebrate
|
||||
organism_function affects experimental_model_of_disease
|
||||
manufactured_object causes mental_or_behavioral_dysfunction
|
||||
cell part_of body_part_organ_or_organ_component
|
||||
molecular_function result_of experimental_model_of_disease
|
||||
medical_device treats acquired_abnormality
|
||||
disease_or_syndrome affects human
|
||||
body_part_organ_or_organ_component location_of molecular_function
|
||||
disease_or_syndrome occurs_in neoplastic_process
|
||||
vitamin isa chemical_viewed_functionally
|
||||
cell_component issue_in occupation_or_discipline
|
||||
cell_component produces nucleic_acid_nucleoside_or_nucleotide
|
||||
bacterium isa organism
|
||||
cell_or_molecular_dysfunction occurs_in injury_or_poisoning
|
||||
hazardous_or_poisonous_substance issue_in occupation_or_discipline
|
||||
organization location_of educational_activity
|
||||
tissue produces biologically_active_substance
|
||||
fungus isa physical_object
|
||||
organism_function result_of phenomenon_or_process
|
||||
organism_function isa biologic_function
|
||||
organic_chemical interacts_with nucleic_acid_nucleoside_or_nucleotide
|
||||
organic_chemical affects natural_phenomenon_or_process
|
||||
diagnostic_procedure associated_with neoplastic_process
|
||||
molecular_function produces neuroreactive_substance_or_biogenic_amine
|
||||
mental_or_behavioral_dysfunction process_of bird
|
||||
chemical_viewed_structurally affects biologic_function
|
||||
experimental_model_of_disease produces biologically_active_substance
|
||||
mental_or_behavioral_dysfunction associated_with organism_attribute
|
||||
laboratory_procedure analyzes neuroreactive_substance_or_biogenic_amine
|
||||
organic_chemical isa substance
|
||||
mental_or_behavioral_dysfunction affects plant
|
||||
daily_or_recreational_activity associated_with experimental_model_of_disease
|
||||
mental_process precedes organ_or_tissue_function
|
||||
chemical affects neoplastic_process
|
||||
hormone ingredient_of clinical_drug
|
||||
hormone isa biologically_active_substance
|
||||
molecular_biology_research_technique measures receptor
|
||||
experimental_model_of_disease precedes neoplastic_process
|
||||
pharmacologic_substance interacts_with neuroreactive_substance_or_biogenic_amine
|
||||
virus interacts_with fish
|
||||
acquired_abnormality affects virus
|
||||
pathologic_function result_of molecular_function
|
||||
embryonic_structure location_of fungus
|
||||
pharmacologic_substance affects cell_or_molecular_dysfunction
|
||||
biologic_function result_of acquired_abnormality
|
||||
neoplastic_process co-occurs_with anatomical_abnormality
|
||||
neoplastic_process result_of acquired_abnormality
|
||||
body_part_organ_or_organ_component produces body_substance
|
||||
cell_or_molecular_dysfunction process_of mental_or_behavioral_dysfunction
|
||||
educational_activity issue_in occupation_or_discipline
|
||||
pathologic_function manifestation_of neoplastic_process
|
||||
virus causes pathologic_function
|
||||
injury_or_poisoning complicates experimental_model_of_disease
|
||||
eicosanoid interacts_with pharmacologic_substance
|
||||
molecular_function result_of natural_phenomenon_or_process
|
||||
neoplastic_process produces tissue
|
||||
diagnostic_procedure assesses_effect_of vitamin
|
||||
anatomical_abnormality manifestation_of organ_or_tissue_function
|
||||
hazardous_or_poisonous_substance ingredient_of clinical_drug
|
||||
organophosphorus_compound affects cell_or_molecular_dysfunction
|
||||
laboratory_procedure measures organism_attribute
|
||||
chemical_viewed_functionally interacts_with immunologic_factor
|
||||
diagnostic_procedure diagnoses disease_or_syndrome
|
||||
injury_or_poisoning complicates disease_or_syndrome
|
||||
molecular_function result_of congenital_abnormality
|
||||
biologic_function affects bacterium
|
||||
organism_function produces hormone
|
||||
individual_behavior associated_with neoplastic_process
|
||||
natural_phenomenon_or_process affects cell_function
|
||||
daily_or_recreational_activity associated_with pathologic_function
|
||||
fully_formed_anatomical_structure location_of rickettsia_or_chlamydia
|
||||
organ_or_tissue_function affects pathologic_function
|
||||
neoplastic_process affects amphibian
|
||||
acquired_abnormality occurs_in age_group
|
||||
mental_process affects organism_attribute
|
||||
molecular_biology_research_technique measures neoplastic_process
|
||||
disease_or_syndrome occurs_in patient_or_disabled_group
|
||||
mental_or_behavioral_dysfunction affects mammal
|
||||
environmental_effect_of_humans isa phenomenon_or_process
|
||||
cell_or_molecular_dysfunction precedes experimental_model_of_disease
|
||||
laboratory_or_test_result isa entity
|
||||
virus interacts_with archaeon
|
||||
indicator_reagent_or_diagnostic_aid causes mental_or_behavioral_dysfunction
|
||||
anatomical_structure part_of fungus
|
||||
cell_or_molecular_dysfunction process_of bird
|
||||
5216
data/umls/train.txt
Normal file
5216
data/umls/train.txt
Normal file
File diff suppressed because it is too large
Load Diff
652
data/umls/valid.txt
Normal file
652
data/umls/valid.txt
Normal file
@ -0,0 +1,652 @@
|
||||
nucleic_acid_nucleoside_or_nucleotide affects mental_or_behavioral_dysfunction
|
||||
patient_or_disabled_group performs individual_behavior
|
||||
neoplastic_process process_of molecular_function
|
||||
lipid affects biologic_function
|
||||
neoplastic_process affects alga
|
||||
antibiotic affects cell_or_molecular_dysfunction
|
||||
eicosanoid affects mental_or_behavioral_dysfunction
|
||||
fully_formed_anatomical_structure location_of injury_or_poisoning
|
||||
machine_activity method_of laboratory_procedure
|
||||
cell_or_molecular_dysfunction isa pathologic_function
|
||||
molecular_biology_research_technique measures organism_function
|
||||
organism_function affects animal
|
||||
patient_or_disabled_group performs governmental_or_regulatory_activity
|
||||
laboratory_procedure measures mental_process
|
||||
tissue surrounds body_space_or_junction
|
||||
anatomical_abnormality affects organism_function
|
||||
plant location_of biologically_active_substance
|
||||
pathologic_function degree_of mental_or_behavioral_dysfunction
|
||||
rickettsia_or_chlamydia location_of neuroreactive_substance_or_biogenic_amine
|
||||
steroid causes anatomical_abnormality
|
||||
organophosphorus_compound isa organic_chemical
|
||||
amino_acid_peptide_or_protein interacts_with eicosanoid
|
||||
age_group produces research_device
|
||||
acquired_abnormality result_of genetic_function
|
||||
organic_chemical interacts_with chemical
|
||||
invertebrate interacts_with fish
|
||||
gene_or_genome produces nucleic_acid_nucleoside_or_nucleotide
|
||||
enzyme isa biologically_active_substance
|
||||
cell location_of body_space_or_junction
|
||||
clinical_attribute degree_of organism_attribute
|
||||
vitamin isa biologically_active_substance
|
||||
animal interacts_with mammal
|
||||
injury_or_poisoning result_of experimental_model_of_disease
|
||||
organism_function co-occurs_with physiologic_function
|
||||
amino_acid_peptide_or_protein interacts_with biologically_active_substance
|
||||
pharmacologic_substance disrupts cell_function
|
||||
mental_process process_of bird
|
||||
acquired_abnormality result_of social_behavior
|
||||
research_activity measures temporal_concept
|
||||
steroid isa substance
|
||||
molecular_function process_of cell_function
|
||||
professional_or_occupational_group performs health_care_activity
|
||||
disease_or_syndrome result_of physiologic_function
|
||||
body_location_or_region location_of injury_or_poisoning
|
||||
antibiotic complicates acquired_abnormality
|
||||
organophosphorus_compound interacts_with amino_acid_peptide_or_protein
|
||||
neuroreactive_substance_or_biogenic_amine complicates injury_or_poisoning
|
||||
gene_or_genome produces body_substance
|
||||
injury_or_poisoning associated_with clinical_attribute
|
||||
cell_function affects human
|
||||
finding associated_with injury_or_poisoning
|
||||
laboratory_procedure measures organic_chemical
|
||||
disease_or_syndrome result_of mental_or_behavioral_dysfunction
|
||||
physiologic_function precedes mental_process
|
||||
body_space_or_junction issue_in occupation_or_discipline
|
||||
mental_or_behavioral_dysfunction process_of animal
|
||||
acquired_abnormality result_of physiologic_function
|
||||
acquired_abnormality result_of injury_or_poisoning
|
||||
idea_or_concept isa conceptual_entity
|
||||
molecular_function process_of archaeon
|
||||
anatomical_abnormality result_of organism_function
|
||||
health_care_related_organization location_of molecular_biology_research_technique
|
||||
eicosanoid causes neoplastic_process
|
||||
pathologic_function precedes neoplastic_process
|
||||
environmental_effect_of_humans result_of injury_or_poisoning
|
||||
element_ion_or_isotope causes neoplastic_process
|
||||
molecular_function affects vertebrate
|
||||
neuroreactive_substance_or_biogenic_amine causes acquired_abnormality
|
||||
steroid causes congenital_abnormality
|
||||
inorganic_chemical interacts_with chemical
|
||||
tissue produces nucleic_acid_nucleoside_or_nucleotide
|
||||
body_part_organ_or_organ_component location_of cell_function
|
||||
organism_attribute property_of animal
|
||||
eicosanoid interacts_with indicator_reagent_or_diagnostic_aid
|
||||
disease_or_syndrome affects mental_process
|
||||
cell_or_molecular_dysfunction process_of disease_or_syndrome
|
||||
pathologic_function result_of biologic_function
|
||||
finding manifestation_of mental_or_behavioral_dysfunction
|
||||
congenital_abnormality location_of bacterium
|
||||
biomedical_or_dental_material causes neoplastic_process
|
||||
chemical_viewed_functionally interacts_with biomedical_or_dental_material
|
||||
experimental_model_of_disease process_of disease_or_syndrome
|
||||
pathologic_function affects experimental_model_of_disease
|
||||
receptor complicates pathologic_function
|
||||
chemical_viewed_structurally affects experimental_model_of_disease
|
||||
fish exhibits individual_behavior
|
||||
immunologic_factor isa entity
|
||||
diagnostic_procedure measures molecular_function
|
||||
carbohydrate isa entity
|
||||
pathologic_function process_of plant
|
||||
amino_acid_sequence property_of gene_or_genome
|
||||
cell_or_molecular_dysfunction affects biologic_function
|
||||
food isa entity
|
||||
neoplastic_process process_of human
|
||||
hazardous_or_poisonous_substance complicates anatomical_abnormality
|
||||
body_location_or_region location_of disease_or_syndrome
|
||||
cell_function process_of animal
|
||||
natural_phenomenon_or_process affects organ_or_tissue_function
|
||||
neuroreactive_substance_or_biogenic_amine isa chemical_viewed_functionally
|
||||
organophosphorus_compound interacts_with element_ion_or_isotope
|
||||
genetic_function result_of disease_or_syndrome
|
||||
neoplastic_process process_of invertebrate
|
||||
laboratory_procedure assesses_effect_of experimental_model_of_disease
|
||||
alga isa organism
|
||||
clinical_attribute measurement_of organ_or_tissue_function
|
||||
human isa entity
|
||||
molecular_sequence isa idea_or_concept
|
||||
hazardous_or_poisonous_substance affects molecular_function
|
||||
amino_acid_peptide_or_protein isa chemical_viewed_structurally
|
||||
age_group issue_in biomedical_occupation_or_discipline
|
||||
laboratory_or_test_result measurement_of element_ion_or_isotope
|
||||
organization location_of laboratory_procedure
|
||||
steroid isa organic_chemical
|
||||
therapeutic_or_preventive_procedure affects disease_or_syndrome
|
||||
natural_phenomenon_or_process result_of organ_or_tissue_function
|
||||
chemical_viewed_functionally causes anatomical_abnormality
|
||||
geographic_area associated_with injury_or_poisoning
|
||||
carbohydrate_sequence result_of mental_process
|
||||
genetic_function result_of environmental_effect_of_humans
|
||||
biomedical_or_dental_material affects cell_or_molecular_dysfunction
|
||||
chemical_viewed_functionally affects pathologic_function
|
||||
molecular_function affects archaeon
|
||||
neoplastic_process manifestation_of organ_or_tissue_function
|
||||
tissue produces neuroreactive_substance_or_biogenic_amine
|
||||
indicator_reagent_or_diagnostic_aid causes cell_or_molecular_dysfunction
|
||||
laboratory_or_test_result evaluation_of mental_process
|
||||
biomedical_or_dental_material causes cell_or_molecular_dysfunction
|
||||
neoplastic_process result_of organ_or_tissue_function
|
||||
genetic_function produces neuroreactive_substance_or_biogenic_amine
|
||||
mental_or_behavioral_dysfunction result_of organ_or_tissue_function
|
||||
mental_process affects invertebrate
|
||||
indicator_reagent_or_diagnostic_aid affects natural_phenomenon_or_process
|
||||
mental_or_behavioral_dysfunction associated_with pathologic_function
|
||||
mental_process affects neoplastic_process
|
||||
cell_function affects biologic_function
|
||||
experimental_model_of_disease manifestation_of genetic_function
|
||||
inorganic_chemical causes congenital_abnormality
|
||||
laboratory_or_test_result measurement_of organic_chemical
|
||||
physical_object isa entity
|
||||
body_location_or_region location_of pathologic_function
|
||||
neuroreactive_substance_or_biogenic_amine complicates cell_function
|
||||
research_activity affects mental_process
|
||||
laboratory_procedure measures pathologic_function
|
||||
amino_acid_peptide_or_protein causes cell_or_molecular_dysfunction
|
||||
acquired_abnormality affects human
|
||||
diagnostic_procedure affects pathologic_function
|
||||
immunologic_factor complicates cell_or_molecular_dysfunction
|
||||
bacterium issue_in biomedical_occupation_or_discipline
|
||||
receptor complicates genetic_function
|
||||
neoplastic_process complicates experimental_model_of_disease
|
||||
organ_or_tissue_function affects cell_function
|
||||
therapeutic_or_preventive_procedure isa health_care_activity
|
||||
experimental_model_of_disease result_of social_behavior
|
||||
therapeutic_or_preventive_procedure method_of biomedical_occupation_or_discipline
|
||||
eicosanoid affects mental_process
|
||||
drug_delivery_device causes congenital_abnormality
|
||||
organism_function affects rickettsia_or_chlamydia
|
||||
mental_or_behavioral_dysfunction produces enzyme
|
||||
manufactured_object causes neoplastic_process
|
||||
chemical_viewed_structurally interacts_with immunologic_factor
|
||||
cell_function process_of fungus
|
||||
physiologic_function process_of invertebrate
|
||||
natural_phenomenon_or_process result_of congenital_abnormality
|
||||
vitamin complicates congenital_abnormality
|
||||
gene_or_genome part_of body_part_organ_or_organ_component
|
||||
disease_or_syndrome result_of phenomenon_or_process
|
||||
disease_or_syndrome affects animal
|
||||
patient_or_disabled_group performs occupational_activity
|
||||
organism_attribute result_of organism_function
|
||||
biologically_active_substance affects pathologic_function
|
||||
embryonic_structure location_of experimental_model_of_disease
|
||||
vitamin affects physiologic_function
|
||||
medical_device causes cell_or_molecular_dysfunction
|
||||
research_activity measures antibiotic
|
||||
drug_delivery_device treats acquired_abnormality
|
||||
organism isa physical_object
|
||||
molecular_function process_of fungus
|
||||
physiologic_function result_of organ_or_tissue_function
|
||||
antibiotic prevents disease_or_syndrome
|
||||
medical_device causes mental_or_behavioral_dysfunction
|
||||
nucleic_acid_nucleoside_or_nucleotide affects mental_process
|
||||
cell_or_molecular_dysfunction process_of physiologic_function
|
||||
chemical affects mental_or_behavioral_dysfunction
|
||||
nucleic_acid_nucleoside_or_nucleotide interacts_with neuroreactive_substance_or_biogenic_amine
|
||||
plant interacts_with bacterium
|
||||
organic_chemical interacts_with chemical_viewed_functionally
|
||||
experimental_model_of_disease associated_with clinical_attribute
|
||||
congenital_abnormality part_of organism
|
||||
gene_or_genome location_of experimental_model_of_disease
|
||||
body_part_organ_or_organ_component location_of fungus
|
||||
amino_acid_peptide_or_protein affects pathologic_function
|
||||
genetic_function produces hormone
|
||||
laboratory_procedure associated_with anatomical_abnormality
|
||||
antibiotic causes pathologic_function
|
||||
acquired_abnormality affects physiologic_function
|
||||
professional_or_occupational_group isa group
|
||||
sign_or_symptom associated_with acquired_abnormality
|
||||
enzyme causes congenital_abnormality
|
||||
genetic_function process_of cell_function
|
||||
vitamin complicates physiologic_function
|
||||
clinical_attribute measurement_of molecular_function
|
||||
embryonic_structure location_of mental_or_behavioral_dysfunction
|
||||
injury_or_poisoning result_of phenomenon_or_process
|
||||
chemical_viewed_structurally affects natural_phenomenon_or_process
|
||||
cell_function affects mental_or_behavioral_dysfunction
|
||||
mental_process affects social_behavior
|
||||
biologic_function process_of virus
|
||||
diagnostic_procedure analyzes indicator_reagent_or_diagnostic_aid
|
||||
experimental_model_of_disease affects physiologic_function
|
||||
virus location_of receptor
|
||||
qualitative_concept evaluation_of health_care_activity
|
||||
cell_function affects alga
|
||||
mental_or_behavioral_dysfunction process_of biologic_function
|
||||
mental_process process_of organ_or_tissue_function
|
||||
organ_or_tissue_function result_of injury_or_poisoning
|
||||
neoplastic_process precedes cell_or_molecular_dysfunction
|
||||
disease_or_syndrome degree_of mental_or_behavioral_dysfunction
|
||||
patient_or_disabled_group produces medical_device
|
||||
antibiotic interacts_with chemical
|
||||
disease_or_syndrome manifestation_of neoplastic_process
|
||||
cell_function process_of organism_function
|
||||
organism_attribute manifestation_of cell_function
|
||||
alga issue_in biomedical_occupation_or_discipline
|
||||
professional_society issue_in biomedical_occupation_or_discipline
|
||||
phenomenon_or_process result_of organism_function
|
||||
chemical affects organism_function
|
||||
laboratory_or_test_result manifestation_of organism_function
|
||||
congenital_abnormality affects organism_function
|
||||
daily_or_recreational_activity associated_with injury_or_poisoning
|
||||
laboratory_or_test_result measurement_of enzyme
|
||||
congenital_abnormality part_of bird
|
||||
neoplastic_process manifestation_of mental_process
|
||||
laboratory_procedure analyzes chemical_viewed_structurally
|
||||
disease_or_syndrome result_of biologic_function
|
||||
hormone disrupts cell
|
||||
cell_or_molecular_dysfunction manifestation_of molecular_function
|
||||
age_group produces regulation_or_law
|
||||
mental_process affects bird
|
||||
medical_device treats mental_or_behavioral_dysfunction
|
||||
phenomenon_or_process result_of mental_process
|
||||
embryonic_structure part_of virus
|
||||
molecular_function affects reptile
|
||||
therapeutic_or_preventive_procedure prevents experimental_model_of_disease
|
||||
lipid isa substance
|
||||
laboratory_procedure assesses_effect_of physiologic_function
|
||||
fish interacts_with organism
|
||||
plant isa physical_object
|
||||
gene_or_genome isa entity
|
||||
clinical_attribute property_of invertebrate
|
||||
diagnostic_procedure analyzes element_ion_or_isotope
|
||||
antibiotic affects natural_phenomenon_or_process
|
||||
gene_or_genome produces vitamin
|
||||
neoplastic_process affects natural_phenomenon_or_process
|
||||
neoplastic_process result_of health_care_activity
|
||||
diagnostic_procedure measures receptor
|
||||
bacterium interacts_with archaeon
|
||||
physiologic_function affects organism_attribute
|
||||
hormone interacts_with receptor
|
||||
professional_society carries_out laboratory_procedure
|
||||
cell location_of organ_or_tissue_function
|
||||
amino_acid_peptide_or_protein ingredient_of clinical_drug
|
||||
human_caused_phenomenon_or_process result_of natural_phenomenon_or_process
|
||||
research_activity issue_in occupation_or_discipline
|
||||
chemical_viewed_functionally causes acquired_abnormality
|
||||
reptile isa vertebrate
|
||||
biologic_function affects invertebrate
|
||||
neoplastic_process affects organism
|
||||
vitamin affects natural_phenomenon_or_process
|
||||
antibiotic diagnoses disease_or_syndrome
|
||||
acquired_abnormality manifestation_of physiologic_function
|
||||
pharmacologic_substance isa chemical
|
||||
age_group exhibits social_behavior
|
||||
organism_function process_of animal
|
||||
professional_or_occupational_group performs machine_activity
|
||||
experimental_model_of_disease isa event
|
||||
neoplastic_process process_of disease_or_syndrome
|
||||
acquired_abnormality location_of disease_or_syndrome
|
||||
event issue_in biomedical_occupation_or_discipline
|
||||
mental_or_behavioral_dysfunction occurs_in professional_or_occupational_group
|
||||
indicator_reagent_or_diagnostic_aid affects experimental_model_of_disease
|
||||
mental_or_behavioral_dysfunction isa biologic_function
|
||||
health_care_activity method_of occupation_or_discipline
|
||||
element_ion_or_isotope affects experimental_model_of_disease
|
||||
plant interacts_with fungus
|
||||
patient_or_disabled_group issue_in occupation_or_discipline
|
||||
self_help_or_relief_organization carries_out occupational_activity
|
||||
research_activity measures molecular_function
|
||||
acquired_abnormality part_of amphibian
|
||||
receptor affects mental_process
|
||||
nucleic_acid_nucleoside_or_nucleotide causes injury_or_poisoning
|
||||
cell_or_molecular_dysfunction affects organ_or_tissue_function
|
||||
organism_attribute result_of experimental_model_of_disease
|
||||
pathologic_function affects bacterium
|
||||
professional_society location_of health_care_activity
|
||||
hazardous_or_poisonous_substance disrupts embryonic_structure
|
||||
animal exhibits social_behavior
|
||||
biologic_function result_of congenital_abnormality
|
||||
pathologic_function affects mental_process
|
||||
diagnostic_procedure measures amino_acid_peptide_or_protein
|
||||
molecular_function co-occurs_with physiologic_function
|
||||
family_group uses medical_device
|
||||
group performs machine_activity
|
||||
laboratory_procedure associated_with pathologic_function
|
||||
neoplastic_process co-occurs_with congenital_abnormality
|
||||
laboratory_procedure measures indicator_reagent_or_diagnostic_aid
|
||||
anatomical_abnormality result_of pathologic_function
|
||||
body_location_or_region location_of cell_function
|
||||
research_activity measures steroid
|
||||
invertebrate causes neoplastic_process
|
||||
laboratory_procedure analyzes hormone
|
||||
disease_or_syndrome affects biologic_function
|
||||
pathologic_function affects genetic_function
|
||||
tissue issue_in occupation_or_discipline
|
||||
biologic_function affects plant
|
||||
anatomical_abnormality affects reptile
|
||||
body_location_or_region location_of mental_or_behavioral_dysfunction
|
||||
medical_device treats pathologic_function
|
||||
organism_attribute result_of cell_function
|
||||
gene_or_genome location_of virus
|
||||
gene_or_genome part_of tissue
|
||||
tissue produces hormone
|
||||
laboratory_or_test_result indicates neoplastic_process
|
||||
mental_or_behavioral_dysfunction complicates injury_or_poisoning
|
||||
biologically_active_substance causes experimental_model_of_disease
|
||||
therapeutic_or_preventive_procedure issue_in biomedical_occupation_or_discipline
|
||||
quantitative_concept measurement_of body_location_or_region
|
||||
professional_or_occupational_group isa entity
|
||||
gene_or_genome affects organ_or_tissue_function
|
||||
eicosanoid affects disease_or_syndrome
|
||||
immunologic_factor complicates organism_function
|
||||
gene_or_genome part_of reptile
|
||||
laboratory_or_test_result manifestation_of molecular_function
|
||||
mental_or_behavioral_dysfunction occurs_in family_group
|
||||
therapeutic_or_preventive_procedure treats mental_or_behavioral_dysfunction
|
||||
population_group isa group
|
||||
body_location_or_region location_of tissue
|
||||
quantitative_concept measurement_of molecular_sequence
|
||||
laboratory_procedure isa activity
|
||||
diagnostic_procedure assesses_effect_of organophosphorus_compound
|
||||
gene_or_genome issue_in occupation_or_discipline
|
||||
organ_or_tissue_function process_of reptile
|
||||
geographic_area isa conceptual_entity
|
||||
neuroreactive_substance_or_biogenic_amine affects mental_or_behavioral_dysfunction
|
||||
biologically_active_substance isa chemical
|
||||
enzyme disrupts embryonic_structure
|
||||
virus location_of vitamin
|
||||
professional_or_occupational_group uses regulation_or_law
|
||||
experimental_model_of_disease result_of therapeutic_or_preventive_procedure
|
||||
indicator_reagent_or_diagnostic_aid causes neoplastic_process
|
||||
sign_or_symptom evaluation_of biologic_function
|
||||
physiologic_function process_of amphibian
|
||||
classification issue_in biomedical_occupation_or_discipline
|
||||
organism_function produces biologically_active_substance
|
||||
laboratory_or_test_result measurement_of chemical
|
||||
immunologic_factor disrupts body_part_organ_or_organ_component
|
||||
health_care_activity issue_in biomedical_occupation_or_discipline
|
||||
carbohydrate interacts_with antibiotic
|
||||
neoplastic_process result_of diagnostic_procedure
|
||||
mental_or_behavioral_dysfunction result_of organism_function
|
||||
cell_component location_of organ_or_tissue_function
|
||||
organophosphorus_compound issue_in occupation_or_discipline
|
||||
cell_component location_of experimental_model_of_disease
|
||||
lipid causes acquired_abnormality
|
||||
experimental_model_of_disease result_of mental_process
|
||||
anatomical_abnormality result_of cell_or_molecular_dysfunction
|
||||
cell_function isa physiologic_function
|
||||
acquired_abnormality manifestation_of cell_function
|
||||
laboratory_or_test_result associated_with disease_or_syndrome
|
||||
mental_process produces hormone
|
||||
mammal exhibits behavior
|
||||
daily_or_recreational_activity associated_with neoplastic_process
|
||||
clinical_drug causes injury_or_poisoning
|
||||
research_activity associated_with pathologic_function
|
||||
cell_or_molecular_dysfunction process_of human
|
||||
body_part_organ_or_organ_component part_of invertebrate
|
||||
drug_delivery_device treats sign_or_symptom
|
||||
neuroreactive_substance_or_biogenic_amine affects disease_or_syndrome
|
||||
vertebrate isa physical_object
|
||||
experimental_model_of_disease result_of diagnostic_procedure
|
||||
drug_delivery_device isa entity
|
||||
therapeutic_or_preventive_procedure uses clinical_drug
|
||||
enzyme affects cell_or_molecular_dysfunction
|
||||
diagnostic_procedure analyzes neuroreactive_substance_or_biogenic_amine
|
||||
amphibian exhibits individual_behavior
|
||||
mental_or_behavioral_dysfunction process_of physiologic_function
|
||||
laboratory_procedure diagnoses cell_or_molecular_dysfunction
|
||||
therapeutic_or_preventive_procedure complicates mental_process
|
||||
steroid interacts_with inorganic_chemical
|
||||
physiologic_function affects plant
|
||||
biomedical_occupation_or_discipline isa conceptual_entity
|
||||
laboratory_procedure analyzes carbohydrate
|
||||
eicosanoid interacts_with receptor
|
||||
age_group performs molecular_biology_research_technique
|
||||
element_ion_or_isotope interacts_with enzyme
|
||||
hazardous_or_poisonous_substance disrupts cell_component
|
||||
congenital_abnormality result_of physiologic_function
|
||||
organophosphorus_compound interacts_with neuroreactive_substance_or_biogenic_amine
|
||||
anatomical_abnormality part_of bacterium
|
||||
clinical_drug causes anatomical_abnormality
|
||||
body_space_or_junction issue_in biomedical_occupation_or_discipline
|
||||
therapeutic_or_preventive_procedure affects mental_process
|
||||
health_care_activity associated_with injury_or_poisoning
|
||||
molecular_function precedes organ_or_tissue_function
|
||||
health_care_related_organization carries_out research_activity
|
||||
cell_function process_of molecular_function
|
||||
neoplastic_process affects experimental_model_of_disease
|
||||
diagnostic_procedure affects cell_or_molecular_dysfunction
|
||||
diagnostic_procedure issue_in occupation_or_discipline
|
||||
governmental_or_regulatory_activity method_of biomedical_occupation_or_discipline
|
||||
laboratory_or_test_result manifestation_of cell_function
|
||||
professional_or_occupational_group produces regulation_or_law
|
||||
laboratory_or_test_result measurement_of pharmacologic_substance
|
||||
pharmacologic_substance affects experimental_model_of_disease
|
||||
receptor affects cell_function
|
||||
neuroreactive_substance_or_biogenic_amine causes anatomical_abnormality
|
||||
body_part_organ_or_organ_component produces vitamin
|
||||
hormone affects biologic_function
|
||||
fully_formed_anatomical_structure location_of disease_or_syndrome
|
||||
receptor affects physiologic_function
|
||||
research_activity measures organism_attribute
|
||||
finding manifestation_of organ_or_tissue_function
|
||||
mental_or_behavioral_dysfunction manifestation_of physiologic_function
|
||||
health_care_activity affects mental_or_behavioral_dysfunction
|
||||
antibiotic interacts_with immunologic_factor
|
||||
disease_or_syndrome produces body_substance
|
||||
diagnostic_procedure measures biomedical_or_dental_material
|
||||
chemical affects natural_phenomenon_or_process
|
||||
research_activity measures biomedical_or_dental_material
|
||||
body_part_organ_or_organ_component conceptual_part_of body_system
|
||||
disease_or_syndrome affects bacterium
|
||||
chemical causes anatomical_abnormality
|
||||
organism_function result_of mental_process
|
||||
cell_or_molecular_dysfunction occurs_in age_group
|
||||
pathologic_function affects amphibian
|
||||
molecular_function isa phenomenon_or_process
|
||||
laboratory_procedure analyzes vitamin
|
||||
governmental_or_regulatory_activity associated_with pathologic_function
|
||||
mental_process result_of acquired_abnormality
|
||||
tissue produces organophosphorus_compound
|
||||
gene_or_genome part_of cell_component
|
||||
mental_or_behavioral_dysfunction affects animal
|
||||
immunologic_factor causes acquired_abnormality
|
||||
antibiotic treats acquired_abnormality
|
||||
eicosanoid isa lipid
|
||||
neuroreactive_substance_or_biogenic_amine causes pathologic_function
|
||||
antibiotic treats congenital_abnormality
|
||||
acquired_abnormality part_of plant
|
||||
mental_or_behavioral_dysfunction process_of mental_process
|
||||
professional_or_occupational_group exhibits individual_behavior
|
||||
cell_component location_of biologic_function
|
||||
hazardous_or_poisonous_substance isa chemical_viewed_functionally
|
||||
cell_function result_of molecular_function
|
||||
element_ion_or_isotope ingredient_of clinical_drug
|
||||
acquired_abnormality affects amphibian
|
||||
group uses classification
|
||||
organic_chemical interacts_with eicosanoid
|
||||
receptor isa biologically_active_substance
|
||||
biologically_active_substance affects molecular_function
|
||||
pathologic_function precedes mental_or_behavioral_dysfunction
|
||||
laboratory_procedure assesses_effect_of biologically_active_substance
|
||||
cell_function produces hormone
|
||||
biologically_active_substance disrupts embryonic_structure
|
||||
biologic_function produces receptor
|
||||
alga location_of hormone
|
||||
experimental_model_of_disease produces receptor
|
||||
organ_or_tissue_function occurs_in mental_process
|
||||
nucleic_acid_nucleoside_or_nucleotide affects molecular_function
|
||||
acquired_abnormality part_of rickettsia_or_chlamydia
|
||||
medical_device treats experimental_model_of_disease
|
||||
neoplastic_process process_of experimental_model_of_disease
|
||||
geographic_area associated_with cell_or_molecular_dysfunction
|
||||
organophosphorus_compound interacts_with steroid
|
||||
cell_function isa natural_phenomenon_or_process
|
||||
disease_or_syndrome result_of social_behavior
|
||||
mental_or_behavioral_dysfunction occurs_in patient_or_disabled_group
|
||||
injury_or_poisoning occurs_in professional_or_occupational_group
|
||||
hazardous_or_poisonous_substance complicates congenital_abnormality
|
||||
invertebrate causes pathologic_function
|
||||
acquired_abnormality occurs_in professional_or_occupational_group
|
||||
lipid affects mental_or_behavioral_dysfunction
|
||||
clinical_attribute associated_with organism_attribute
|
||||
lipid affects mental_process
|
||||
invertebrate interacts_with reptile
|
||||
gene_or_genome part_of vertebrate
|
||||
organ_or_tissue_function process_of mammal
|
||||
body_substance conceptual_part_of body_system
|
||||
body_part_organ_or_organ_component produces neuroreactive_substance_or_biogenic_amine
|
||||
carbohydrate interacts_with inorganic_chemical
|
||||
anatomical_abnormality part_of mammal
|
||||
natural_phenomenon_or_process affects molecular_function
|
||||
substance causes cell_or_molecular_dysfunction
|
||||
embryonic_structure surrounds cell
|
||||
injury_or_poisoning isa phenomenon_or_process
|
||||
diagnostic_procedure diagnoses anatomical_abnormality
|
||||
body_space_or_junction location_of injury_or_poisoning
|
||||
cell_function result_of experimental_model_of_disease
|
||||
neuroreactive_substance_or_biogenic_amine complicates genetic_function
|
||||
experimental_model_of_disease result_of environmental_effect_of_humans
|
||||
health_care_activity affects cell_or_molecular_dysfunction
|
||||
professional_society carries_out diagnostic_procedure
|
||||
health_care_activity affects mental_process
|
||||
group produces research_device
|
||||
cell_component location_of congenital_abnormality
|
||||
vertebrate isa animal
|
||||
molecular_biology_research_technique measures biomedical_or_dental_material
|
||||
professional_society produces classification
|
||||
amino_acid_sequence isa idea_or_concept
|
||||
genetic_function co-occurs_with physiologic_function
|
||||
mental_or_behavioral_dysfunction manifestation_of genetic_function
|
||||
biologic_function process_of mammal
|
||||
individual_behavior affects social_behavior
|
||||
pathologic_function co-occurs_with injury_or_poisoning
|
||||
invertebrate causes experimental_model_of_disease
|
||||
fish interacts_with archaeon
|
||||
research_device causes disease_or_syndrome
|
||||
quantitative_concept issue_in biomedical_occupation_or_discipline
|
||||
professional_society location_of therapeutic_or_preventive_procedure
|
||||
drug_delivery_device prevents disease_or_syndrome
|
||||
fully_formed_anatomical_structure part_of invertebrate
|
||||
mammal isa entity
|
||||
body_part_organ_or_organ_component produces receptor
|
||||
molecular_function affects mammal
|
||||
laboratory_procedure analyzes biomedical_or_dental_material
|
||||
human_caused_phenomenon_or_process isa phenomenon_or_process
|
||||
experimental_model_of_disease process_of vertebrate
|
||||
professional_society carries_out research_activity
|
||||
experimental_model_of_disease precedes cell_or_molecular_dysfunction
|
||||
experimental_model_of_disease affects amphibian
|
||||
laboratory_procedure assesses_effect_of hazardous_or_poisonous_substance
|
||||
anatomical_abnormality issue_in biomedical_occupation_or_discipline
|
||||
hormone affects mental_process
|
||||
laboratory_procedure analyzes pharmacologic_substance
|
||||
body_location_or_region location_of genetic_function
|
||||
disease_or_syndrome result_of injury_or_poisoning
|
||||
laboratory_procedure assesses_effect_of neoplastic_process
|
||||
congenital_abnormality affects animal
|
||||
biomedical_or_dental_material interacts_with immunologic_factor
|
||||
organism_function isa natural_phenomenon_or_process
|
||||
classification isa intellectual_product
|
||||
natural_phenomenon_or_process result_of anatomical_abnormality
|
||||
chemical_viewed_functionally affects neoplastic_process
|
||||
amino_acid_sequence result_of mental_process
|
||||
clinical_attribute property_of reptile
|
||||
mammal exhibits individual_behavior
|
||||
natural_phenomenon_or_process affects disease_or_syndrome
|
||||
organ_or_tissue_function process_of neoplastic_process
|
||||
biologically_active_substance complicates mental_process
|
||||
laboratory_procedure assesses_effect_of biomedical_or_dental_material
|
||||
biomedical_or_dental_material interacts_with chemical
|
||||
neoplastic_process associated_with cell_or_molecular_dysfunction
|
||||
qualitative_concept isa idea_or_concept
|
||||
sign_or_symptom evaluation_of experimental_model_of_disease
|
||||
neuroreactive_substance_or_biogenic_amine interacts_with receptor
|
||||
cell location_of pathologic_function
|
||||
diagnostic_procedure assesses_effect_of enzyme
|
||||
acquired_abnormality part_of alga
|
||||
organophosphorus_compound interacts_with hazardous_or_poisonous_substance
|
||||
diagnostic_procedure assesses_effect_of lipid
|
||||
fungus interacts_with invertebrate
|
||||
laboratory_or_test_result measurement_of physiologic_function
|
||||
acquired_abnormality affects mental_process
|
||||
disease_or_syndrome affects reptile
|
||||
amino_acid_sequence isa entity
|
||||
mental_process result_of biologic_function
|
||||
organic_chemical affects biologic_function
|
||||
steroid interacts_with hormone
|
||||
pathologic_function result_of acquired_abnormality
|
||||
research_activity measures chemical_viewed_structurally
|
||||
therapeutic_or_preventive_procedure associated_with mental_or_behavioral_dysfunction
|
||||
physiologic_function result_of mental_process
|
||||
clinical_attribute result_of human_caused_phenomenon_or_process
|
||||
laboratory_procedure measures antibiotic
|
||||
cell part_of invertebrate
|
||||
vitamin complicates cell_or_molecular_dysfunction
|
||||
clinical_attribute manifestation_of molecular_function
|
||||
organism_function result_of acquired_abnormality
|
||||
professional_or_occupational_group interacts_with age_group
|
||||
natural_phenomenon_or_process affects neoplastic_process
|
||||
organization carries_out research_activity
|
||||
embryonic_structure part_of bacterium
|
||||
fully_formed_anatomical_structure produces enzyme
|
||||
organic_chemical interacts_with indicator_reagent_or_diagnostic_aid
|
||||
natural_phenomenon_or_process result_of human_caused_phenomenon_or_process
|
||||
neoplastic_process affects pathologic_function
|
||||
fully_formed_anatomical_structure issue_in biomedical_occupation_or_discipline
|
||||
environmental_effect_of_humans result_of experimental_model_of_disease
|
||||
experimental_model_of_disease manifestation_of physiologic_function
|
||||
body_part_organ_or_organ_component location_of mental_process
|
||||
receptor causes injury_or_poisoning
|
||||
sign_or_symptom diagnoses disease_or_syndrome
|
||||
antibiotic disrupts mental_process
|
||||
mental_process precedes organism_function
|
||||
chemical_viewed_structurally affects cell_or_molecular_dysfunction
|
||||
vitamin disrupts molecular_function
|
||||
pharmacologic_substance causes injury_or_poisoning
|
||||
professional_or_occupational_group performs governmental_or_regulatory_activity
|
||||
educational_activity isa activity
|
||||
congenital_abnormality location_of disease_or_syndrome
|
||||
neoplastic_process co-occurs_with pathologic_function
|
||||
chemical_viewed_functionally causes mental_or_behavioral_dysfunction
|
||||
biologic_function process_of human
|
||||
hormone complicates mental_or_behavioral_dysfunction
|
||||
embryonic_structure location_of rickettsia_or_chlamydia
|
||||
congenital_abnormality result_of mental_or_behavioral_dysfunction
|
||||
organ_or_tissue_function produces enzyme
|
||||
molecular_biology_research_technique measures experimental_model_of_disease
|
||||
disease_or_syndrome process_of organism_function
|
||||
finding manifestation_of disease_or_syndrome
|
||||
pathologic_function process_of mammal
|
||||
organ_or_tissue_function process_of human
|
||||
indicator_reagent_or_diagnostic_aid affects physiologic_function
|
||||
health_care_related_organization carries_out molecular_biology_research_technique
|
||||
hazardous_or_poisonous_substance disrupts organ_or_tissue_function
|
||||
mental_process process_of invertebrate
|
||||
tissue location_of experimental_model_of_disease
|
||||
antibiotic isa pharmacologic_substance
|
||||
therapeutic_or_preventive_procedure prevents mental_or_behavioral_dysfunction
|
||||
steroid affects disease_or_syndrome
|
||||
pharmacologic_substance prevents disease_or_syndrome
|
||||
behavior result_of mental_process
|
||||
social_behavior associated_with geographic_area
|
||||
tissue part_of body_part_organ_or_organ_component
|
||||
molecular_function affects rickettsia_or_chlamydia
|
||||
population_group performs governmental_or_regulatory_activity
|
||||
biologically_active_substance disrupts organism_function
|
||||
acquired_abnormality isa anatomical_abnormality
|
||||
molecular_function affects alga
|
||||
congenital_abnormality result_of human_caused_phenomenon_or_process
|
||||
congenital_abnormality result_of environmental_effect_of_humans
|
||||
neoplastic_process process_of mental_or_behavioral_dysfunction
|
||||
functional_concept isa entity
|
||||
spatial_concept isa conceptual_entity
|
||||
mental_or_behavioral_dysfunction process_of cell_or_molecular_dysfunction
|
||||
biomedical_or_dental_material causes anatomical_abnormality
|
||||
hazardous_or_poisonous_substance causes congenital_abnormality
|
||||
antibiotic disrupts cell
|
||||
disease_or_syndrome affects alga
|
||||
finding manifestation_of experimental_model_of_disease
|
||||
element_ion_or_isotope affects natural_phenomenon_or_process
|
||||
amphibian interacts_with archaeon
|
||||
body_space_or_junction location_of mental_process
|
||||
substance causes neoplastic_process
|
||||
biologic_function affects genetic_function
|
||||
indicator_reagent_or_diagnostic_aid causes injury_or_poisoning
|
||||
research_activity measures pharmacologic_substance
|
||||
injury_or_poisoning result_of environmental_effect_of_humans
|
||||
organization issue_in occupation_or_discipline
|
||||
organ_or_tissue_function process_of mental_process
|
||||
research_activity associated_with mental_or_behavioral_dysfunction
|
||||
human issue_in biomedical_occupation_or_discipline
|
||||
molecular_function affects disease_or_syndrome
|
||||
eicosanoid affects pathologic_function
|
||||
Reference in New Issue
Block a user