diff --git a/src/mappings/pato_attribute_value.sssom.tsv b/src/mappings/pato_attribute_value.sssom.tsv new file mode 100644 index 00000000..6353ffa5 --- /dev/null +++ b/src/mappings/pato_attribute_value.sssom.tsv @@ -0,0 +1,400 @@ +# curie_map: +# PATO: http://purl.obolibrary.org/obo/PATO_ +# owl: http://www.w3.org/2002/07/owl# +# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# +# rdfs: http://www.w3.org/2000/01/rdf-schema# +# semapv: https://w3id.org/semapv/ +# skos: http://www.w3.org/2004/02/skos/core# +# sssom: https://w3id.org/sssom/ +# license: https://creativecommons.org/publicdomain/zero/1.0/ +# mapping_date: '2023-03-24' +# mapping_set_id: http://purl.obolibrary.org/obo/oba/mappings/pato_attribute_value.sssom.tsv +# object_source: http://purl.obolibrary.org/obo/pato.owl +# subject_source: http://purl.obolibrary.org/obo/pato.owl +subject_id subject_label predicate_id object_id mapping_justification +PATO:0000303 increased speed skos:broadMatch PATO:0000008 semapv:UnspecifiedMatching +PATO:0000304 decreased speed skos:broadMatch PATO:0000008 semapv:UnspecifiedMatching +PATO:0000330 irregular spatial pattern skos:broadMatch PATO:0000060 semapv:UnspecifiedMatching +PATO:0000374 increased distance skos:broadMatch PATO:0000040 semapv:UnspecifiedMatching +PATO:0000375 decreased distance skos:broadMatch PATO:0000040 semapv:UnspecifiedMatching +PATO:0000380 increased frequency skos:broadMatch PATO:0000044 semapv:UnspecifiedMatching +PATO:0000381 decreased frequency skos:broadMatch PATO:0000044 semapv:UnspecifiedMatching +PATO:0000394 mild intensity skos:broadMatch PATO:0000049 semapv:UnspecifiedMatching +PATO:0000395 moderate intensity skos:broadMatch PATO:0000049 semapv:UnspecifiedMatching +PATO:0000396 severe intensity skos:broadMatch PATO:0000049 semapv:UnspecifiedMatching +PATO:0000440 regular spatial pattern skos:broadMatch PATO:0000060 semapv:UnspecifiedMatching +PATO:0000470 increased amount skos:broadMatch PATO:0000070 semapv:UnspecifiedMatching +PATO:0000498 increased duration skos:broadMatch PATO:0001309 semapv:UnspecifiedMatching +PATO:0000499 decreased duration skos:broadMatch PATO:0001309 semapv:UnspecifiedMatching +PATO:0000500 advanced phase skos:broadMatch PATO:0000083 semapv:UnspecifiedMatching +PATO:0000501 dark phase skos:broadMatch PATO:0000083 semapv:UnspecifiedMatching +PATO:0000503 light phase skos:broadMatch PATO:0000083 semapv:UnspecifiedMatching +PATO:0000569 decreased height skos:broadMatch PATO:0000119 semapv:UnspecifiedMatching +PATO:0000570 increased height skos:broadMatch PATO:0000119 semapv:UnspecifiedMatching +PATO:0000573 increased length skos:broadMatch PATO:0000122 semapv:UnspecifiedMatching +PATO:0000574 decreased length skos:broadMatch PATO:0000122 semapv:UnspecifiedMatching +PATO:0000582 increased weight skos:broadMatch PATO:0000128 semapv:UnspecifiedMatching +PATO:0000583 decreased weight skos:broadMatch PATO:0000128 semapv:UnspecifiedMatching +PATO:0000586 increased size skos:broadMatch PATO:0000117 semapv:UnspecifiedMatching +PATO:0000587 decreased size skos:broadMatch PATO:0000117 semapv:UnspecifiedMatching +PATO:0000591 increased thickness skos:broadMatch PATO:0000915 semapv:UnspecifiedMatching +PATO:0000592 decreased thickness skos:broadMatch PATO:0000915 semapv:UnspecifiedMatching +PATO:0000595 increased volume skos:broadMatch PATO:0000918 semapv:UnspecifiedMatching +PATO:0000596 decreased volume skos:broadMatch PATO:0000918 semapv:UnspecifiedMatching +PATO:0000599 decreased width skos:broadMatch PATO:0000921 semapv:UnspecifiedMatching +PATO:0000600 increased width skos:broadMatch PATO:0000921 semapv:UnspecifiedMatching +PATO:0000706 increased threshold skos:broadMatch PATO:0000152 semapv:UnspecifiedMatching +PATO:0000708 decreased threshold skos:broadMatch PATO:0000152 semapv:UnspecifiedMatching +PATO:0000760 increased behavioural activity skos:broadMatch PATO:0002265 semapv:UnspecifiedMatching +PATO:0000761 decreased behavioural activity skos:broadMatch PATO:0002265 semapv:UnspecifiedMatching +PATO:0000911 decreased rate skos:broadMatch PATO:0000161 semapv:UnspecifiedMatching +PATO:0000912 increased rate skos:broadMatch PATO:0000161 semapv:UnspecifiedMatching +PATO:0001054 internal angle skos:broadMatch PATO:0002326 semapv:UnspecifiedMatching +PATO:0001305 increased temperature skos:broadMatch PATO:0000146 semapv:UnspecifiedMatching +PATO:0001306 decreased temperature skos:broadMatch PATO:0000146 semapv:UnspecifiedMatching +PATO:0001307 decreased variability of temperature skos:broadMatch PATO:0001304 semapv:UnspecifiedMatching +PATO:0001308 increased variability of temperature skos:broadMatch PATO:0001304 semapv:UnspecifiedMatching +PATO:0001311 decreased duration of temperature skos:broadMatch PATO:0001310 semapv:UnspecifiedMatching +PATO:0001312 increased duration of temperature skos:broadMatch PATO:0001310 semapv:UnspecifiedMatching +PATO:0001315 mild increased temperature skos:broadMatch PATO:0000146 semapv:UnspecifiedMatching +PATO:0001316 moderate increased temperature skos:broadMatch PATO:0000146 semapv:UnspecifiedMatching +PATO:0001317 severe increased temperature skos:broadMatch PATO:0000146 semapv:UnspecifiedMatching +PATO:0001324 bilateral symmetry skos:broadMatch PATO:0000965 semapv:UnspecifiedMatching +PATO:0001347 F mating type skos:broadMatch PATO:0001895 semapv:UnspecifiedMatching +PATO:0001348 F minus mating type skos:broadMatch PATO:0001895 semapv:UnspecifiedMatching +PATO:0001416 regular duration skos:broadMatch PATO:0001309 semapv:UnspecifiedMatching +PATO:0001417 irregular duration skos:broadMatch PATO:0001309 semapv:UnspecifiedMatching +PATO:0001472 decreased depth skos:broadMatch PATO:0001595 semapv:UnspecifiedMatching +PATO:0001475 increased position skos:broadMatch PATO:0000140 semapv:UnspecifiedMatching +PATO:0001476 decreased position skos:broadMatch PATO:0000140 semapv:UnspecifiedMatching +PATO:0001542 delayed phase skos:broadMatch PATO:0000083 semapv:UnspecifiedMatching +PATO:0001549 increased sensitivity toward skos:broadMatch PATO:0000085 semapv:UnspecifiedMatching +PATO:0001550 decreased sensitivity toward skos:broadMatch PATO:0000085 semapv:UnspecifiedMatching +PATO:0001551 increased sensitivity of a process skos:broadMatch PATO:0001457 semapv:UnspecifiedMatching +PATO:0001552 decreased sensitivity of a process skos:broadMatch PATO:0001457 semapv:UnspecifiedMatching +PATO:0001553 increased sensitivity of a process to oxygen skos:broadMatch PATO:0001458 semapv:UnspecifiedMatching +PATO:0001554 decreased sensitivity of a process to oxygen skos:broadMatch PATO:0001458 semapv:UnspecifiedMatching +PATO:0001562 decreased mass skos:broadMatch PATO:0000125 semapv:UnspecifiedMatching +PATO:0001563 increased mass skos:broadMatch PATO:0000125 semapv:UnspecifiedMatching +PATO:0001575 decreased pressure skos:broadMatch PATO:0001025 semapv:UnspecifiedMatching +PATO:0001576 increased pressure skos:broadMatch PATO:0001025 semapv:UnspecifiedMatching +PATO:0001577 increased permeability skos:broadMatch PATO:0000970 semapv:UnspecifiedMatching +PATO:0001578 decreased permeability skos:broadMatch PATO:0000970 semapv:UnspecifiedMatching +PATO:0001580 increased contractility skos:broadMatch PATO:0001579 semapv:UnspecifiedMatching +PATO:0001581 decreased contractility skos:broadMatch PATO:0001579 semapv:UnspecifiedMatching +PATO:0001583 decreased variability skos:broadMatch PATO:0001303 semapv:UnspecifiedMatching +PATO:0001584 increased variability skos:broadMatch PATO:0001303 semapv:UnspecifiedMatching +PATO:0001592 increased curvature skos:broadMatch PATO:0001591 semapv:UnspecifiedMatching +PATO:0001593 decreased curvature skos:broadMatch PATO:0001591 semapv:UnspecifiedMatching +PATO:0001596 increased depth skos:broadMatch PATO:0001595 semapv:UnspecifiedMatching +PATO:0001603 increased life span skos:broadMatch PATO:0000050 semapv:UnspecifiedMatching +PATO:0001604 decreased life span skos:broadMatch PATO:0000050 semapv:UnspecifiedMatching +PATO:0001612 increased variability of color skos:broadMatch PATO:0001611 semapv:UnspecifiedMatching +PATO:0001613 decreased variability of color skos:broadMatch PATO:0001611 semapv:UnspecifiedMatching +PATO:0001618 increased tonicity skos:broadMatch PATO:0001439 semapv:UnspecifiedMatching +PATO:0001619 decreased tonicity skos:broadMatch PATO:0001439 semapv:UnspecifiedMatching +PATO:0001621 decreased turgor skos:broadMatch PATO:0001620 semapv:UnspecifiedMatching +PATO:0001622 increased turgor skos:broadMatch PATO:0001620 semapv:UnspecifiedMatching +PATO:0001624 decreased functionality skos:broadMatch PATO:0001509 semapv:UnspecifiedMatching +PATO:0001625 increased functionality skos:broadMatch PATO:0001509 semapv:UnspecifiedMatching +PATO:0001650 increased resistance to skos:broadMatch PATO:0001046 semapv:UnspecifiedMatching +PATO:0001651 decreased resistance to skos:broadMatch PATO:0001046 semapv:UnspecifiedMatching +PATO:0001656 decreased osmolarity skos:broadMatch PATO:0001655 semapv:UnspecifiedMatching +PATO:0001657 increased osmolarity skos:broadMatch PATO:0001655 semapv:UnspecifiedMatching +PATO:0001663 increased solubility skos:broadMatch PATO:0001536 semapv:UnspecifiedMatching +PATO:0001664 decreased solubility skos:broadMatch PATO:0001536 semapv:UnspecifiedMatching +PATO:0001669 increased susceptibility toward skos:broadMatch PATO:0001043 semapv:UnspecifiedMatching +PATO:0001670 decreased susceptibility toward skos:broadMatch PATO:0001043 semapv:UnspecifiedMatching +PATO:0001675 decreased efficiency skos:broadMatch PATO:0001029 semapv:UnspecifiedMatching +PATO:0001676 increased efficiency skos:broadMatch PATO:0001029 semapv:UnspecifiedMatching +PATO:0001683 increased magnetism skos:broadMatch PATO:0001682 semapv:UnspecifiedMatching +PATO:0001684 decreased magnetism skos:broadMatch PATO:0001682 semapv:UnspecifiedMatching +PATO:0001688 increased elevation skos:broadMatch PATO:0001687 semapv:UnspecifiedMatching +PATO:0001689 decreased elevation skos:broadMatch PATO:0001687 semapv:UnspecifiedMatching +PATO:0001693 increased viscosity skos:broadMatch PATO:0000992 semapv:UnspecifiedMatching +PATO:0001694 decreased viscosity skos:broadMatch PATO:0000992 semapv:UnspecifiedMatching +PATO:0001695 increased fecundity skos:broadMatch PATO:0000273 semapv:UnspecifiedMatching +PATO:0001696 decreased fecundity skos:broadMatch PATO:0000273 semapv:UnspecifiedMatching +PATO:0001697 decreased photosensitivity skos:broadMatch PATO:0000927 semapv:UnspecifiedMatching +PATO:0001698 increased photosensitivity skos:broadMatch PATO:0000927 semapv:UnspecifiedMatching +PATO:0001699 regular sleep pattern skos:broadMatch PATO:0000062 semapv:UnspecifiedMatching +PATO:0001700 irregular sleep pattern skos:broadMatch PATO:0000062 semapv:UnspecifiedMatching +PATO:0001712 increased perimeter skos:broadMatch PATO:0001711 semapv:UnspecifiedMatching +PATO:0001713 decreased perimeter skos:broadMatch PATO:0001711 semapv:UnspecifiedMatching +PATO:0001714 increased diameter skos:broadMatch PATO:0001334 semapv:UnspecifiedMatching +PATO:0001715 decreased diameter skos:broadMatch PATO:0001334 semapv:UnspecifiedMatching +PATO:0001723 increased female receptivity skos:broadMatch PATO:0001719 semapv:UnspecifiedMatching +PATO:0001723 increased female receptivity skos:broadMatch PATO:0001720 semapv:UnspecifiedMatching +PATO:0001724 decreased female receptivity skos:broadMatch PATO:0001719 semapv:UnspecifiedMatching +PATO:0001724 decreased female receptivity skos:broadMatch PATO:0001720 semapv:UnspecifiedMatching +PATO:0001725 increased male receptivity skos:broadMatch PATO:0001719 semapv:UnspecifiedMatching +PATO:0001725 increased male receptivity skos:broadMatch PATO:0001721 semapv:UnspecifiedMatching +PATO:0001726 decreased male receptivity skos:broadMatch PATO:0001719 semapv:UnspecifiedMatching +PATO:0001726 decreased male receptivity skos:broadMatch PATO:0001721 semapv:UnspecifiedMatching +PATO:0001764 increased age skos:broadMatch PATO:0000011 semapv:UnspecifiedMatching +PATO:0001765 decreased age skos:broadMatch PATO:0000011 semapv:UnspecifiedMatching +PATO:0001776 increased flexibility skos:broadMatch PATO:0001543 semapv:UnspecifiedMatching +PATO:0001777 decreased flexibility skos:broadMatch PATO:0001543 semapv:UnspecifiedMatching +PATO:0001778 increased strength skos:broadMatch PATO:0001230 semapv:UnspecifiedMatching +PATO:0001779 decreased strength skos:broadMatch PATO:0001230 semapv:UnspecifiedMatching +PATO:0001781 irregular thickness skos:broadMatch PATO:0000915 semapv:UnspecifiedMatching +PATO:0001782 increased intensity skos:broadMatch PATO:0000049 semapv:UnspecifiedMatching +PATO:0001783 decreased intensity skos:broadMatch PATO:0000049 semapv:UnspecifiedMatching +PATO:0001787 rotational curvature skos:broadMatch PATO:0001591 semapv:UnspecifiedMatching +PATO:0001788 increased mass density skos:broadMatch PATO:0001019 semapv:UnspecifiedMatching +PATO:0001790 decreased mass density skos:broadMatch PATO:0001019 semapv:UnspecifiedMatching +PATO:0001795 increased coiling skos:broadMatch PATO:0001794 semapv:UnspecifiedMatching +PATO:0001796 decreased coiling skos:broadMatch PATO:0001794 semapv:UnspecifiedMatching +PATO:0001801 decreased water composition skos:broadMatch PATO:0000025 semapv:UnspecifiedMatching +PATO:0001801 decreased water composition skos:broadMatch PATO:0001800 semapv:UnspecifiedMatching +PATO:0001807 decreased sensitivity to irradiation skos:broadMatch PATO:0001806 semapv:UnspecifiedMatching +PATO:0001808 increased sensitivity to irradiation skos:broadMatch PATO:0001806 semapv:UnspecifiedMatching +PATO:0001816 increased fatigability skos:broadMatch PATO:0001815 semapv:UnspecifiedMatching +PATO:0001817 decreased fatigability skos:broadMatch PATO:0001815 semapv:UnspecifiedMatching +PATO:0001825 increased wetness skos:broadMatch PATO:0001822 semapv:UnspecifiedMatching +PATO:0001826 decreased wetness skos:broadMatch PATO:0001822 semapv:UnspecifiedMatching +PATO:0001830 decreased female fertility skos:broadMatch PATO:0000274 semapv:UnspecifiedMatching +PATO:0001830 decreased female fertility skos:broadMatch PATO:0000277 semapv:UnspecifiedMatching +PATO:0001831 increased female fertility skos:broadMatch PATO:0000277 semapv:UnspecifiedMatching +PATO:0001831 increased female fertility skos:broadMatch PATO:0000274 semapv:UnspecifiedMatching +PATO:0001832 increased male fertility skos:broadMatch PATO:0000274 semapv:UnspecifiedMatching +PATO:0001832 increased male fertility skos:broadMatch PATO:0000279 semapv:UnspecifiedMatching +PATO:0001833 decreased male fertility skos:broadMatch PATO:0000274 semapv:UnspecifiedMatching +PATO:0001833 decreased male fertility skos:broadMatch PATO:0000279 semapv:UnspecifiedMatching +PATO:0001834 decreased fertility skos:broadMatch PATO:0000274 semapv:UnspecifiedMatching +PATO:0001835 increased fertility skos:broadMatch PATO:0000274 semapv:UnspecifiedMatching +PATO:0001841 remittent intensity skos:broadMatch PATO:0000049 semapv:UnspecifiedMatching +PATO:0001843 decreased acidity skos:broadMatch PATO:0001842 semapv:UnspecifiedMatching +PATO:0001844 increased acidity skos:broadMatch PATO:0001842 semapv:UnspecifiedMatching +PATO:0001859 increased coordination skos:broadMatch PATO:0000188 semapv:UnspecifiedMatching +PATO:0001860 decreased coordination skos:broadMatch PATO:0000188 semapv:UnspecifiedMatching +PATO:0001892 decreased odor skos:broadMatch PATO:0000058 semapv:UnspecifiedMatching +PATO:0001893 increased odor skos:broadMatch PATO:0000058 semapv:UnspecifiedMatching +PATO:0001898 increased circumference skos:broadMatch PATO:0001648 semapv:UnspecifiedMatching +PATO:0001899 decreased circumference skos:broadMatch PATO:0001648 semapv:UnspecifiedMatching +PATO:0001904 circling direction skos:broadMatch PATO:0000039 semapv:UnspecifiedMatching +PATO:0001926 increased fluorescence skos:broadMatch PATO:0000018 semapv:UnspecifiedMatching +PATO:0001927 decreased fluorescence skos:broadMatch PATO:0000018 semapv:UnspecifiedMatching +PATO:0001957 decreased variability of size skos:broadMatch PATO:0001956 semapv:UnspecifiedMatching +PATO:0001958 increased variability of size skos:broadMatch PATO:0001956 semapv:UnspecifiedMatching +PATO:0001997 decreased amount skos:broadMatch PATO:0000070 semapv:UnspecifiedMatching +PATO:0002025 external angle skos:broadMatch PATO:0002326 semapv:UnspecifiedMatching +PATO:0002028 decreased osmolality skos:broadMatch PATO:0002027 semapv:UnspecifiedMatching +PATO:0002029 increased osmolality skos:broadMatch PATO:0002027 semapv:UnspecifiedMatching +PATO:0002042 decreased anterior-posterior diameter skos:broadMatch PATO:0001334 semapv:UnspecifiedMatching +PATO:0002042 decreased anterior-posterior diameter skos:broadMatch PATO:0002041 semapv:UnspecifiedMatching +PATO:0002043 increased anterior-posterior diameter skos:broadMatch PATO:0001334 semapv:UnspecifiedMatching +PATO:0002043 increased anterior-posterior diameter skos:broadMatch PATO:0002041 semapv:UnspecifiedMatching +PATO:0002049 lateral and rotional curvature skos:broadMatch PATO:0001591 semapv:UnspecifiedMatching +PATO:0002050 normal amount skos:broadMatch PATO:0000070 semapv:UnspecifiedMatching +PATO:0002051 increased occurrence skos:broadMatch PATO:0000057 semapv:UnspecifiedMatching +PATO:0002052 decreased occurrence skos:broadMatch PATO:0000057 semapv:UnspecifiedMatching +PATO:0002055 increased fragility skos:broadMatch PATO:0001662 semapv:UnspecifiedMatching +PATO:0002056 decreased fragility skos:broadMatch PATO:0001662 semapv:UnspecifiedMatching +PATO:0002057 increased area skos:broadMatch PATO:0001323 semapv:UnspecifiedMatching +PATO:0002058 decreased area skos:broadMatch PATO:0001323 semapv:UnspecifiedMatching +PATO:0002071 increased affinity skos:broadMatch PATO:0002070 semapv:UnspecifiedMatching +PATO:0002072 decreased affinity skos:broadMatch PATO:0002070 semapv:UnspecifiedMatching +PATO:0002074 increased avidity skos:broadMatch PATO:0002073 semapv:UnspecifiedMatching +PATO:0002075 decreased avidity skos:broadMatch PATO:0002073 semapv:UnspecifiedMatching +PATO:0002144 increased radiopacity skos:broadMatch PATO:0002136 semapv:UnspecifiedMatching +PATO:0002145 decreased radiopacity skos:broadMatch PATO:0002136 semapv:UnspecifiedMatching +PATO:0002147 reduced virulence skos:broadMatch PATO:0002146 semapv:UnspecifiedMatching +PATO:0002148 increased virulence skos:broadMatch PATO:0002146 semapv:UnspecifiedMatching +PATO:0002187 polar polarity skos:broadMatch PATO:0002186 semapv:UnspecifiedMatching +PATO:0002188 nonpolar polarity skos:broadMatch PATO:0002186 semapv:UnspecifiedMatching +PATO:0002202 left handedness skos:broadMatch PATO:0002201 semapv:UnspecifiedMatching +PATO:0002203 right handedness skos:broadMatch PATO:0002201 semapv:UnspecifiedMatching +PATO:0002204 ambidextrous handedness skos:broadMatch PATO:0002201 semapv:UnspecifiedMatching +PATO:0002221 increased phosphorylation skos:broadMatch PATO:0002262 semapv:UnspecifiedMatching +PATO:0002222 decreased phosphorylation skos:broadMatch PATO:0002262 semapv:UnspecifiedMatching +PATO:0002245 increased force skos:broadMatch PATO:0001035 semapv:UnspecifiedMatching +PATO:0002246 decreased force skos:broadMatch PATO:0001035 semapv:UnspecifiedMatching +PATO:0002266 3-D shape skos:broadMatch PATO:0000052 semapv:UnspecifiedMatching +PATO:0002267 edge shape skos:broadMatch PATO:0000052 semapv:UnspecifiedMatching +PATO:0002270 increased accumulation skos:broadMatch PATO:0002269 semapv:UnspecifiedMatching +PATO:0002271 decreased accumulation skos:broadMatch PATO:0002269 semapv:UnspecifiedMatching +PATO:0002275 high contrast color pattern skos:broadMatch PATO:0000019 semapv:UnspecifiedMatching +PATO:0002282 increased mobility skos:broadMatch PATO:0000004 semapv:UnspecifiedMatching +PATO:0002283 decreased mobility skos:broadMatch PATO:0000004 semapv:UnspecifiedMatching +PATO:0002285 increased branchiness skos:broadMatch PATO:0002009 semapv:UnspecifiedMatching +PATO:0002286 decreased branchiness skos:broadMatch PATO:0002009 semapv:UnspecifiedMatching +PATO:0002287 increased elasticity skos:broadMatch PATO:0001031 semapv:UnspecifiedMatching +PATO:0002288 decreased elasticity skos:broadMatch PATO:0001031 semapv:UnspecifiedMatching +PATO:0002297 decreased cellular motility skos:broadMatch PATO:0001488 semapv:UnspecifiedMatching +PATO:0002298 increased cellular motility skos:broadMatch PATO:0001488 semapv:UnspecifiedMatching +PATO:0002315 brush-like shape skos:broadMatch PATO:0000052 semapv:UnspecifiedMatching +PATO:0002333 increased adhesivity skos:broadMatch PATO:0001431 semapv:UnspecifiedMatching +PATO:0002334 decreased adhesivity skos:broadMatch PATO:0001431 semapv:UnspecifiedMatching +PATO:0002361 increased tendency skos:broadMatch PATO:0002360 semapv:UnspecifiedMatching +PATO:0002362 decreased tendency skos:broadMatch PATO:0002360 semapv:UnspecifiedMatching +PATO:0002382 increased waxiness skos:broadMatch PATO:0002381 semapv:UnspecifiedMatching +PATO:0002383 decreased waxiness skos:broadMatch PATO:0002381 semapv:UnspecifiedMatching +PATO:0002471 increased velocity skos:broadMatch PATO:0002242 semapv:UnspecifiedMatching +PATO:0002472 decreased velocity skos:broadMatch PATO:0002242 semapv:UnspecifiedMatching +PATO:0002481 oblique orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002490 anterior orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002491 anterodorsal orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002492 anterolateral orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002493 anteroventral orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002494 distal orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002495 dorsal orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002496 dorsolateral orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002497 lateral orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002498 medial orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002499 posterior orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002500 ventrolaterally orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002501 ventral orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002502 transverse orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002503 posterolateral orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002504 posterodorsal orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002514 anteromedial orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002524 mesiolateral orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002526 anterodistal orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002527 posterodistal orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0002628 borderline intensity skos:broadMatch PATO:0000049 semapv:UnspecifiedMatching +PATO:0002629 profound intensity skos:broadMatch PATO:0000049 semapv:UnspecifiedMatching +PATO:0005012 complete structure skos:broadMatch PATO:0000141 semapv:UnspecifiedMatching +PATO:0005013 incomplete structure skos:broadMatch PATO:0000141 semapv:UnspecifiedMatching +PATO:0005015 tapered size skos:broadMatch PATO:0000117 semapv:UnspecifiedMatching +PATO:0005022 uniform diameter skos:broadMatch PATO:0001334 semapv:UnspecifiedMatching +PATO:0005023 parasagittal orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0005024 longitudinal orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0010006 cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0015001 absence due to degeneration skos:broadMatch PATO:0002037 semapv:UnspecifiedMatching +PATO:0015010 increased humidity skos:broadMatch PATO:0015009 semapv:UnspecifiedMatching +PATO:0015011 decreased humidity skos:broadMatch PATO:0015009 semapv:UnspecifiedMatching +PATO:0015014 increased degree of illumination skos:broadMatch PATO:0015013 semapv:UnspecifiedMatching +PATO:0015015 decreased degree of illumination skos:broadMatch PATO:0015013 semapv:UnspecifiedMatching +PATO:0015022 increased combustibility skos:broadMatch PATO:0015021 semapv:UnspecifiedMatching +PATO:0015023 decreased combustibility skos:broadMatch PATO:0015021 semapv:UnspecifiedMatching +PATO:0015024 increased porosity skos:broadMatch PATO:0000973 semapv:UnspecifiedMatching +PATO:0015025 decreased porosity skos:broadMatch PATO:0000973 semapv:UnspecifiedMatching +PATO:0015027 increased stability skos:broadMatch PATO:0015026 semapv:UnspecifiedMatching +PATO:0015028 decreased stability skos:broadMatch PATO:0015026 semapv:UnspecifiedMatching +PATO:0015032 increased contamination skos:broadMatch PATO:0015031 semapv:UnspecifiedMatching +PATO:0015033 decreased contamination skos:broadMatch PATO:0015031 semapv:UnspecifiedMatching +PATO:0040005 posteroventral orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0040013 dorsomedial orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0040023 distomedial orientation skos:broadMatch PATO:0000133 semapv:UnspecifiedMatching +PATO:0040030 decreased width and length skos:broadMatch PATO:0000122 semapv:UnspecifiedMatching +PATO:0040031 increased width and length skos:broadMatch PATO:0000122 semapv:UnspecifiedMatching +PATO:0040042 decreased proportionality to skos:broadMatch PATO:0001470 semapv:UnspecifiedMatching +PATO:0040043 increased proportionality to skos:broadMatch PATO:0001470 semapv:UnspecifiedMatching +PATO:0040045 population growth rate skos:broadMatch PATO:0000161 semapv:UnspecifiedMatching +PATO:0040045 population growth rate skos:broadMatch PATO:0001492 semapv:UnspecifiedMatching +PATO:0045000 normal rate skos:broadMatch PATO:0000161 semapv:UnspecifiedMatching +PATO:0045002 normal acidity skos:broadMatch PATO:0001842 semapv:UnspecifiedMatching +PATO:0045003 normal adhesivity skos:broadMatch PATO:0001431 semapv:UnspecifiedMatching +PATO:0045004 normal affinity skos:broadMatch PATO:0002070 semapv:UnspecifiedMatching +PATO:0045005 normal age skos:broadMatch PATO:0000011 semapv:UnspecifiedMatching +PATO:0045006 normal avidity skos:broadMatch PATO:0002073 semapv:UnspecifiedMatching +PATO:0045007 normal behavioural activity skos:broadMatch PATO:0002265 semapv:UnspecifiedMatching +PATO:0045008 normal cellular motility skos:broadMatch PATO:0001488 semapv:UnspecifiedMatching +PATO:0045009 normal coiling skos:broadMatch PATO:0001794 semapv:UnspecifiedMatching +PATO:0045011 normal contractility skos:broadMatch PATO:0001579 semapv:UnspecifiedMatching +PATO:0045012 normal coordination skos:broadMatch PATO:0000188 semapv:UnspecifiedMatching +PATO:0045013 normal curvature skos:broadMatch PATO:0001591 semapv:UnspecifiedMatching +PATO:0045014 normal distance skos:broadMatch PATO:0000040 semapv:UnspecifiedMatching +PATO:0045015 normal efficiency skos:broadMatch PATO:0001029 semapv:UnspecifiedMatching +PATO:0045016 normal elasticity skos:broadMatch PATO:0001031 semapv:UnspecifiedMatching +PATO:0045017 normal fecundity skos:broadMatch PATO:0000273 semapv:UnspecifiedMatching +PATO:0045018 normal female fertility skos:broadMatch PATO:0000277 semapv:UnspecifiedMatching +PATO:0045018 normal female fertility skos:broadMatch PATO:0000274 semapv:UnspecifiedMatching +PATO:0045019 normal female receptivity skos:broadMatch PATO:0001719 semapv:UnspecifiedMatching +PATO:0045019 normal female receptivity skos:broadMatch PATO:0001720 semapv:UnspecifiedMatching +PATO:0045020 normal fertility skos:broadMatch PATO:0000274 semapv:UnspecifiedMatching +PATO:0045021 normal flexibility skos:broadMatch PATO:0001543 semapv:UnspecifiedMatching +PATO:0045023 normal fluorescence skos:broadMatch PATO:0000018 semapv:UnspecifiedMatching +PATO:0045024 normal force skos:broadMatch PATO:0001035 semapv:UnspecifiedMatching +PATO:0045025 normal fragility skos:broadMatch PATO:0001662 semapv:UnspecifiedMatching +PATO:0045026 normal life span skos:broadMatch PATO:0000050 semapv:UnspecifiedMatching +PATO:0045027 normal magnetism skos:broadMatch PATO:0001682 semapv:UnspecifiedMatching +PATO:0045028 normal male fertility skos:broadMatch PATO:0000279 semapv:UnspecifiedMatching +PATO:0045028 normal male fertility skos:broadMatch PATO:0000274 semapv:UnspecifiedMatching +PATO:0045029 normal male receptivity skos:broadMatch PATO:0001719 semapv:UnspecifiedMatching +PATO:0045029 normal male receptivity skos:broadMatch PATO:0001721 semapv:UnspecifiedMatching +PATO:0045030 normal mass skos:broadMatch PATO:0000125 semapv:UnspecifiedMatching +PATO:0045031 normal mass density skos:broadMatch PATO:0001019 semapv:UnspecifiedMatching +PATO:0045032 normal mobility skos:broadMatch PATO:0000004 semapv:UnspecifiedMatching +PATO:0045033 normal odor skos:broadMatch PATO:0000058 semapv:UnspecifiedMatching +PATO:0045034 normal osmolality skos:broadMatch PATO:0002027 semapv:UnspecifiedMatching +PATO:0045035 normal osmolarity skos:broadMatch PATO:0001655 semapv:UnspecifiedMatching +PATO:0045036 normal permeability skos:broadMatch PATO:0000970 semapv:UnspecifiedMatching +PATO:0045037 normal phosphorylation skos:broadMatch PATO:0002262 semapv:UnspecifiedMatching +PATO:0045038 normal photosensitivity skos:broadMatch PATO:0000927 semapv:UnspecifiedMatching +PATO:0045040 normal position skos:broadMatch PATO:0000140 semapv:UnspecifiedMatching +PATO:0045043 normal elevation skos:broadMatch PATO:0001687 semapv:UnspecifiedMatching +PATO:0045044 normal pressure skos:broadMatch PATO:0001025 semapv:UnspecifiedMatching +PATO:0045046 normal radiopacity skos:broadMatch PATO:0002136 semapv:UnspecifiedMatching +PATO:0045047 normal resistance to skos:broadMatch PATO:0001046 semapv:UnspecifiedMatching +PATO:0045048 normal sensitivity to irradiation skos:broadMatch PATO:0001806 semapv:UnspecifiedMatching +PATO:0045049 normal sensitivity toward skos:broadMatch PATO:0000085 semapv:UnspecifiedMatching +PATO:0045050 normal size skos:broadMatch PATO:0000117 semapv:UnspecifiedMatching +PATO:0045051 normal area skos:broadMatch PATO:0001323 semapv:UnspecifiedMatching +PATO:0045052 normal depth skos:broadMatch PATO:0001595 semapv:UnspecifiedMatching +PATO:0045053 normal height skos:broadMatch PATO:0000119 semapv:UnspecifiedMatching +PATO:0045054 normal length skos:broadMatch PATO:0000122 semapv:UnspecifiedMatching +PATO:0045055 normal diameter skos:broadMatch PATO:0001334 semapv:UnspecifiedMatching +PATO:0045056 normal anterior-posterior diameter skos:broadMatch PATO:0001334 semapv:UnspecifiedMatching +PATO:0045056 normal anterior-posterior diameter skos:broadMatch PATO:0002041 semapv:UnspecifiedMatching +PATO:0045057 normal perimeter skos:broadMatch PATO:0001711 semapv:UnspecifiedMatching +PATO:0045058 normal circumference skos:broadMatch PATO:0001648 semapv:UnspecifiedMatching +PATO:0045059 normal thickness skos:broadMatch PATO:0000915 semapv:UnspecifiedMatching +PATO:0045060 normal volume skos:broadMatch PATO:0000918 semapv:UnspecifiedMatching +PATO:0045061 normal width skos:broadMatch PATO:0000921 semapv:UnspecifiedMatching +PATO:0045062 normal solubility skos:broadMatch PATO:0001536 semapv:UnspecifiedMatching +PATO:0045063 normal speed skos:broadMatch PATO:0000008 semapv:UnspecifiedMatching +PATO:0045064 normal strength skos:broadMatch PATO:0001230 semapv:UnspecifiedMatching +PATO:0045065 normal fatigability skos:broadMatch PATO:0001815 semapv:UnspecifiedMatching +PATO:0045066 normal susceptibility toward skos:broadMatch PATO:0001043 semapv:UnspecifiedMatching +PATO:0045067 normal temperature skos:broadMatch PATO:0000146 semapv:UnspecifiedMatching +PATO:0045068 normal tendency skos:broadMatch PATO:0002360 semapv:UnspecifiedMatching +PATO:0045069 normal threshold skos:broadMatch PATO:0000152 semapv:UnspecifiedMatching +PATO:0045071 normal tonicity skos:broadMatch PATO:0001439 semapv:UnspecifiedMatching +PATO:0045072 normal turgor skos:broadMatch PATO:0001620 semapv:UnspecifiedMatching +PATO:0045074 normal variability skos:broadMatch PATO:0001303 semapv:UnspecifiedMatching +PATO:0045075 normal variability of color skos:broadMatch PATO:0001611 semapv:UnspecifiedMatching +PATO:0045077 normal variability of size skos:broadMatch PATO:0001956 semapv:UnspecifiedMatching +PATO:0045078 normal variability of temperature skos:broadMatch PATO:0001304 semapv:UnspecifiedMatching +PATO:0045079 normal velocity skos:broadMatch PATO:0002242 semapv:UnspecifiedMatching +PATO:0045080 normal virulence skos:broadMatch PATO:0002146 semapv:UnspecifiedMatching +PATO:0045081 normal viscosity skos:broadMatch PATO:0000992 semapv:UnspecifiedMatching +PATO:0045082 normal waxiness skos:broadMatch PATO:0002381 semapv:UnspecifiedMatching +PATO:0045083 normal wetness skos:broadMatch PATO:0001822 semapv:UnspecifiedMatching +PATO:0045084 normal duration skos:broadMatch PATO:0001309 semapv:UnspecifiedMatching +PATO:0045085 normal duration of temperature skos:broadMatch PATO:0001310 semapv:UnspecifiedMatching +PATO:0045086 normal occurrence skos:broadMatch PATO:0000057 semapv:UnspecifiedMatching +PATO:0045087 normal frequency skos:broadMatch PATO:0000044 semapv:UnspecifiedMatching +PATO:0045088 normal sensitivity of a process skos:broadMatch PATO:0001457 semapv:UnspecifiedMatching +PATO:0045089 normal sensitivity of a process to oxygen skos:broadMatch PATO:0001458 semapv:UnspecifiedMatching +PATO:0045090 cardinal direction skos:broadMatch PATO:0000039 semapv:UnspecifiedMatching +PATO:0070001 neurogliaform morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070002 basket cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070003 small basket cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070004 large basket cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070005 nest basket cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070006 cortical bipolar morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070007 Martinotti morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070008 T Martinotti morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070009 fan Martinotti morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070010 stellate morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070011 chandelier cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070012 bitufted cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070013 spiny stellate cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070015 pyramidal family morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070016 horizontal pyramidal morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070017 standard pyramidal morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070018 tufted pyramidal morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070019 untufted pyramidal morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070020 stellate pyramidal morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070021 inverted pyramidal morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070025 unipolar neuron morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070026 multipolar neuron morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070027 bitufted dendrite cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070042 retinal bipolar morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070061 double bouquet morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070062 bistratified dendrite cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070063 monostratified dendrite cell morphology skos:broadMatch PATO:0000051 semapv:UnspecifiedMatching +PATO:0070064 dendritic field size skos:broadMatch PATO:0000117 semapv:UnspecifiedMatching + diff --git a/src/ontology/oba.Makefile b/src/ontology/oba.Makefile index 6114e8a5..b084ab07 100644 --- a/src/ontology/oba.Makefile +++ b/src/ontology/oba.Makefile @@ -280,8 +280,20 @@ phenotype_mappings: grep -Eo "ZP:[0-9]+" ../mappings/oba-all-phenotype.sssom.tsv | sort | uniq | wc -l grep -Eo "XPO:[0-9]+" ../mappings/oba-all-phenotype.sssom.tsv | sort | uniq | wc -l -q: - echo $() + +tmp/pato.owl: + wget "http://purl.obolibrary.org/obo/pato.owl" -O $@ + +../mappings/pato_attribute_value.csv: tmp/pato.owl ../sparql/pato-attribute-value-map.sparql + $(ROBOT) query -i $< --query ../sparql/pato-attribute-value-map.sparql $@ + +prepare_release: ../mappings/pato_attribute_value.sssom.tsv + +../mappings/pato_attribute_value.sssom.tsv: tmp/pato.owl ../sparql/pato-attribute-value-map.sparql + $(ROBOT) query -i $< --format ttl --query ../sparql/pato-attribute-value-map.ru tmp/construct_pato_attribute.ttl + $(ROBOT) annotate -i tmp/construct_pato_attribute.ttl --ontology-iri "http://purl.obolibrary.org/obo/pato/mappings.owl" convert -f json -o tmp/construct_pato_attribute.json + sssom parse tmp/construct_pato_attribute.json -I obographs-json -C merged -m config/oba.sssom.config.yml -o $@ + sssom annotate $@ --mapping_set_id "http://purl.obolibrary.org/obo/oba/mappings/pato_attribute_value.sssom.tsv" --mapping_date $(TODAY) --subject_source http://purl.obolibrary.org/obo/pato.owl --object_source http://purl.obolibrary.org/obo/pato.owl -o $@ $(TMPDIR)/base_unsat.md: $(TMPDIR)/mirror-all.owl $(ROBOT) explain -i $< -M unsatisfiability --unsatisfiable random:10 --explanation $@ diff --git a/src/sparql/pato-attribute-value-map.ru b/src/sparql/pato-attribute-value-map.ru new file mode 100644 index 00000000..dc10440c --- /dev/null +++ b/src/sparql/pato-attribute-value-map.ru @@ -0,0 +1,42 @@ +PREFIX rdf: +prefix RO: +prefix HP: +prefix PATO: +prefix rdfs: +prefix oio: +prefix def: +prefix owl: +PREFIX xsd: +prefix skos: + + +# Get all classes related to diseases that +CONSTRUCT { + ?parent a owl:Class . + ?entity a owl:Class . + skos:broadMatch a owl:AnnotationProperty . + ?entity rdfs:label ?entity_label . + ?parent rdfs:label ?parent_label . + ?entity skos:broadMatch ?parent . + ?parent rdfs:subClassOf PATO:0000001 . + ?entity rdfs:subClassOf PATO:0000001 . +} + +WHERE +{ + + ?parent rdfs:subClassOf+ PATO:0000001 . + ?parent oio:inSubset . + ?entity rdfs:subClassOf+ ?parent . + ?entity rdfs:label ?entity_label . + ?parent rdfs:label ?parent_label . + + FILTER NOT EXISTS { + ?entity oio:inSubset . + } + + FILTER(STRSTARTS(STR(?entity), "http://purl.obolibrary.org/obo/PATO_")) + FILTER(STRSTARTS(STR(?parent), "http://purl.obolibrary.org/obo/PATO_")) + FILTER(STRENDS(STR(?entity_label), CONCAT(" ",STR(?parent_label)))) +} + \ No newline at end of file diff --git a/src/sparql/pato-attribute-value-map.sparql b/src/sparql/pato-attribute-value-map.sparql new file mode 100644 index 00000000..50cd2d0f --- /dev/null +++ b/src/sparql/pato-attribute-value-map.sparql @@ -0,0 +1,29 @@ +PREFIX rdf: +prefix RO: +prefix HP: +prefix PATO: +prefix rdfs: +prefix oio: +prefix def: +prefix owl: +PREFIX xsd: + +# Get all classes related to diseases that +SELECT DISTINCT ?parent ?parent_label ?entity ?entity_label WHERE +{ + + ?parent rdfs:subClassOf+ PATO:0000001 . + ?parent oio:inSubset . + ?entity rdfs:subClassOf+ ?parent . + ?entity rdfs:label ?entity_label . + ?parent rdfs:label ?parent_label . + + FILTER NOT EXISTS { + ?entity oio:inSubset . + } + + FILTER(STRSTARTS(STR(?entity), "http://purl.obolibrary.org/obo/PATO_")) + FILTER(STRSTARTS(STR(?parent), "http://purl.obolibrary.org/obo/PATO_")) + FILTER(STRENDS(STR(?entity_label), CONCAT(" ",STR(?parent_label)))) +} + \ No newline at end of file