creativeishu / aim_ibm_kgo Goto Github PK

Understand how to get the API key.

Tomorrow morning we quickly have to find good benchmark test cases and than we can try some scaling analysis.

This is low priority. It could speed up the tree navigation.

Deterministic search

1. how does query improve with maxdepth?
2. same question with similarity edges
3. how does it scale with number of threads?

Random walk

1. how does the query improve with the number of walkers?
2. same question with similarities
3. how does it scale with number of threads?

Search in General

1. result quality/search cost without similarity edges
2. result quality/search cost with similarity edges
3. do similarity edges for one property improve search for another property?
4. compare two different thresholds for similarity edge creation.

MIDs for all chemical elements

{u'Ru': u'/m/025scl1', u'Re': u'/m/025scmg', u'Rf': u'/m/025sd1x', u'Rg': u'/m/025tpyw', u'Ra': u'/m/025scm7', u'Rb': u'/m/025sckv', u'Rn': u'/m/025scmp', u'Rh': u'/m/025scm0', u'Be': u'/m/025sq7x', u'Ba': u'/m/025svml', u'Bh': u'/m/025s_py', u'Bi': u'/m/025svp8', u'Bk': u'/m/025svnm', u'Br': u'/m/025svll', u'H': u'/m/02h9byz', u'P': u'/m/025s7x6', u'Os': u'/m/025s6b_', u'Ge': u'/m/025rs3d', u'Gd': u'/m/025rs3m', u'Ga': u'/m/025rs35', u'Pr': u'/m/025sc08', u'Ute': u'/m/07kvy3', u'Pt': u'/m/025s7y2', u'Pu': u'/m/026mkzy', u'C': u'/m/025tfgm', u'Pb': u'/m/025r_0t', u'Pa': u'/m/025s7xw', u'Pd': u'/m/025s7xf', u'Cd': u'/m/025tksd', u'Po': u'/m/025s7y9', u'Pm': u'/m/025s7xn', u'Uut': u'/m/026bqpv', u'Uuq': u'/m/026bqm6', u'Uup': u'/m/025tzk3', u'Uus': u'/m/025tzmz', u'Uuo': u'/m/025tsrz', u'Ho': u'/m/025rtj9', u'Uue': u'/m/0hr4p', u'Hf': u'/m/025rtjj', u'Hg': u'/m/025sw5g', u'He': u'/m/025rt79', u'Md': u'/m/025s0rf', u'Mg': u'/m/025s0s0', u'K': u'/m/02kcq04', u'Mn': u'/m/025s0zp', u'O': u'/m/025s6bf', u'Mt': u'/m/025s2kx', u'S': u'/m/025sf9q', u'W': u'/m/025sk79', u'Zn': u'/m/025sqz8', u'Eu': u'/m/028bf0d', u'Es': u'/m/028bh5n', u'Er': u'/m/028bg3q', u'Ni': u'/m/025s4r7', u'No': u'/m/025s4s4', u'Na': u'/m/02kcq1_', u'Nb': u'/m/025s4rg', u'Nd': u'/m/025s4rp', u'Ne': u'/m/025s4r0', u'Np': u'/m/025s4ry', u'Fr': u'/m/025rqcb', u'Fe': u'/m/02kcv_c', u'Fm': u'/m/025rqck', u'B': u'/m/0bnv6p5', u'F': u'/m/025rqc3', u'Sr': u'/m/025sf8p', u'Uth': u'/m/07kwcp', u'Uto': u'/m/07kvrh', u'N': u'/m/025s4ld', u'Uts': u'/m/05lynv', u'Si': u'/m/025sf80', u'Sn': u'/m/025sk5n', u'Sm': u'/m/025sf93', u'V': u'/m/025sngq', u'Sc': u'/m/025sf87', u'Sb': u'/m/027s2zq', u'Sg': u'/m/025sgk0', u'Se': u'/m/025sf8g', u'Co': u'/m/025tkrf', u'Cn': u'/m/025t_2_', u'Cm': u'/m/025tkv0', u'Cl': u'/m/025tkqp', u'Ca': u'/m/025tkqy', u'Cf': u'/m/025tkv8', u'Ce': u'/m/025tktq', u'Xe': u'/m/025sqqf', u'Tm': u'/m/025sk7j', u'Cs': u'/m/025tnb6', u'Cr': u'/m/025tkr6', u'Cu': u'/m/025rsfk', u'La': u'/m/025rz_s', u'Li': u'/m/025rzqx', u'Lv': u'/m/025tsrr', u'Tl': u'/m/025skld', u'Lu': u'/m/025rz__', u'Lr': u'/m/025r_0l', u'Th': u'/m/025sk62', u'Ti': u'/m/025sk56', u'Te': u'/m/025sk5w', u'Tb': u'/m/025sk71', u'Tc': u'/m/025sk5f', u'Ta': u'/m/025sk7r', u'Ubt': u'/m/04ztzs', u'Ubu': u'/m/047n69', u'Ubp': u'/m/03hft_m', u'Ubq': u'/m/02p6l9k', u'Ubs': u'/m/03hft__', u'Yb': u'/m/025sqvg', u'Db': u'/m/0274b33', u'Zr': u'/m/025sqzx', u'Ubb': u'/m/025rsdc', u'Dy': u'/m/026rjl1', u'Ubn': u'/m/0hr49', u'Ubo': u'/m/02p6lmn', u'Ubh': u'/m/03p6rr', u'Ds': u'/m/025syct', u'I': u'/m/025rw2h', u'In': u'/m/025rw28', u'U': u'/m/025smjn', u'Y': u'/m/025sqv7', u'Ac': u'/m/027sjs4', u'Ag': u'/m/025sf8x', u'Kr': u'/m/0286yf3', u'Ir': u'/m/025rw2y', u'Am': u'/m/027sxty', u'Al': u'/m/027vj2v', u'As': u'/m/027rq1r', u'Ar': u'/m/027r9df', u'Au': u'/m/025rs2z', u'At': u'/m/027t9kn', u'Hs': u'/m/025rtwf', u'Mo': u'/m/025s0zx'}

-- convert smiles to svg,
-- integrate into props
-- can be found in props['smiles_svg']

changing database backend...

Dear everyone,

Hope you all are doing good!!!

I need to free some of my private repositories. So, either I'll have to delete this repository, or make it public, or transfer the ownership to one of you.

Please let me know if anyone of you would like to own this repository. If not, do let me know if anyone of you has any problem deleting or making this repository public.

If possible, please let me know in next couple of days.

Thanks,

Irshad

For example:
Noble gas: /m/01c8fc

Here the full list of categories to check:
http://www.freebase.com/chemistry/chemical_series?instances=

Discoverer: http://www.freebase.com/chemistry/element_discoverer?instances=
Classification: http://www.freebase.com/chemistry/chemical_classification?instances=

According to @delaya and @dev-zero, http://dbpedia.org seems to be quiet incomplete, at least the entries from the Infobox for example for Iron seem to be completely missing.

The best course of action is therefore probably to use the Wikipedia API Library to parse the data directly from the respective Wikipedia pages.

Other options are:

• use a periodic table
• use Freebase

This needs #1 to be implemented.

In depth two Neon should have more connections

Currently we have:

practitioner./education/field_of_study/academics_in_this_field
narrower_than./food/ingredient/more_general_ingredient
broader_than./medicine/drug_brand/canonical_drug
object./freebase/valuenotation/is_reviewed
origin./people/person/place_of_birth
subclass_of./people/cause_of_death/parent_cause_of_death
part_of./biology/gene/genome
certification./award/award_winner/awards_won
member_of./people/person/religion
category./biology/organism_classification/rank
part_of./medicine/drug/marketed_formulations
narrower_than./base/skosbase/skos_concept/broader
symbolizes./location/location_symbol_relationship/administrative_division
category./people/person/ethnicity
practitioner./business/industry/companies
part_of./people/family_member/family
superclass_of./business/product_ingredient/generalization_of
location./people/place_lived/location
certification./award/ranking/list
narrower_than./chemistry/isotope/isotope_of
member_of./royalty/chivalric_order_membership/order
medicine./medicine/disease_cause/diseases
peer_of./influence/peer_relationship/peers
narrower_than./base/skosbase/vocabulary_equivalent_topic/broader_concept
status./medicine/drug/legal_status
category./medicine/drug/mechanism_of_action
member_of./organization/organization_membership/organization
broader_than./base/skosbase/skos_concept/narrower
category./chemistry/chemical_compound/classifications
broader_than./chemistry/chemical_element/isotopes
medicine./medicine/medical_treatment/side_effects
fiction_link./fictional_universe/fictional_substance/fictional_object
parent./people/person/parents
narrower_than./medicine/drug_ingredient/more_general_ingredient
discovered_by./chemistry/chemical_element/discoverer
broader_than./food/ingredient/more_specific_ingredient
superclass_of./engineering/material/subclass
superclass_of./chemistry/chemical_classification/lower_classifications
narrower_than./medicine/drug/canonical_brands
certification./medicine/drug/pregnancy_category
title./royalty/noble_title_tenure/noble_title
subclass_of./chemistry/chemical_classification/higher_classifications
category./chemistry/chemical_element/chemical_series
created./organization/organization_founder/organizations_founded
discovered./chemistry/element_discoverer/discovered
created_by./organization/organization/founders
property./common/topic/image
medicine./medicine/condition_prevention_factors/conditions_this_may_prevent
skos./base/skosbase/skos_concept/in_scheme
peer_of./people/marriage/spouse
member_of./education/academic/departments_old
peer_of./education/academic/advisees
medicine./medicine/risk_factor/diseases
location./biology/gene/chromosome
peer_of./education/academic/advisors
category./biology/gene_group_membership/group
category./location/location_symbol_relationship/Kind_of_symbol
created./book/author/works_written
location./people/deceased_person/place_of_burial
subclass_of./engineering/material/parent_material_class
title./business/employment_tenure/title
category./chemistry/chemical_element/periodic_table_block
certification./education/education/degree
object./freebase/review_item/flag
category./biology/gene_ontology_group/group_type
object./dataworld/gardening_hint/replaces
means_of_demise./people/deceased_person/cause_of_death
owner./business/company_brand_relationship/company
created./law/inventor/inventions
use_permitted_by./spaceflight/rocket_engine_fuel/rocket_engines
part_of./medicine/drug_ingredient/active_ingredient_of_formulation
leader_of./organization/organization_board_membership/organization
created_by./law/invention/inventor
practitioner_of./people/person/profession
medicine./medicine/medical_treatment/contraindications
member_of./people/person/nationality
child./people/person/children
member_of./base/skosbase/skos_concept/in_scheme
category./people/person/gender
subclass_of./business/product_ingredient/variety_of
subclass_of./biology/organism_classification/higher_classification
part_of./organization/organization_relationship/parent
object./type/object/attribution
subclass_of./biology/gene_ontology_group/broader_group
peer_of./base/skosbase/vocabulary_equivalent_topic/equivalent_concept
use_permitted_by./spaceflight/rocket_engine_oxidizer/rocket_engines
peer_of./freebase/equivalent_topic/equivalent_type
object./freebase/valuenotation/has_value
broader_than./base/schemastaging/food_extra/narrower
broader_than./medicine/drug_ingredient/more_specific_ingredient
broader_than./base/skosbase/vocabulary_equivalent_topic/narrower_concept
member_of./business/employment_tenure/company
category./medicine/drug/drug_class
made_of./food/nutrition_fact/nutrient
peer_of./people/sibling_relationship/sibling
leader_of./organization/leadership/organization
medicine./medicine/medical_treatment/used_to_treat
created./people/person/quotations
practitioner_of./education/education/major_field_of_study
member_of./education/education/institution
means_of_demise./chemistry/isotope_decay/decay_mode
practitioner_of./organization/organization_board_membership/role
object./freebase/valuenotation/has_no_value

We need a simple interface to run queries

Should we show the (first few sentences in) the description field of a node?
Perhaps in a small font, in the tooltip?

We need the exact result of the query so that we can compare the approximate methods.

We need to store the data fetched from Wikipedia somewhere.
This does not have to be final store, just such that we have a dataset we can work on.

For examples results of search.